Merge lp:~matttbe/ubuntu/raring/latexmk/v4.35 into lp:ubuntu/raring/latexmk

[Matthieu Baerts]

Hello,

As you can see, Latexmk is available in Debian and Ubuntu repositories but it's an old version (4.24 - released more than one year ago).

A new version has been released less than two months ago and it's still not available in Debian repositories. It seems that the official maintainer doesn't answer to these bugs reports:
 * http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=668926 => [PATCH] latexmk: Helping to update to packaging format 3.0
 * http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=693126 => latexmk: New upstream release available + watch file

Is it possible to upload this new version to Ubuntu repositories because it will be needed by the new version of LaTeXila (and also because it fixes other bugs, please have a look at this debian/changelog file). Or should I first report this bug to another Debian dev? Or is it easier to upload this new version to Ubuntu repos first because Debian Testing migration has been frozen?
This new version has been uploaded to mentors.debian.net but I'm not sure that I'll receive an answer from the official Debian maintainer soon.

Thank you for your help,

Matt

PS: this new version can be easily tested by using this package: https://launchpad.net/~matttbe/+archive/experimental-debian-build/+sourcepub/2900053/+listing-archive-extra

[Andrew Starr-Bochicchio (andrewsomething)]

Looks good, but I did make a few tweaks to the changelog. I condensed it to one entry as the proposed Debian versions haven't actually entered the Debian archive. I also dropped the upstream changelog as it's really more verbose than we need for debian/changelog.

Thanks for your work!

review: Approve

[Matthieu Baerts (matttbe)]

Thank you for these changes and for your support! :)

Matt

Unmerged revisions

9. By Matthieu Baerts on 2012-12-27

* New upstream release. (LP: #1094164)
* Upstream ChangeLog:
  - 4.35 dated 11 November 2012.
    * Corrects bug that fls file is incorrectly parsed when using a
      combination of cygwin and a native MS-Windows TeX program.
    * Corrects bug that old dependency information was retained when using
      the --gg option.
  - 4.34 dated 1 October 2012.
    * Corrects non-optimality that latexmk may do extra runs of (pdf)latex
      when a file is read and written during a run of (pdf)latex, but the
      file is only read after being written.
  - 4.33c dated 19 August 2012.
    * Corrects infinite loop in error messages when the maximum number of
      passes through latex/pdflatex is exceeded.
  - 4.33b dated 12 August 2012.
    * Documentation improvements, including documentation of the many
      options for the (pdf)latex programs that are supported by latexmk.
  - 4.33a dated 8 August 2012.
    * Fix slowness of v. 4.33 under Cygwin.
  - 4.33 dated 6 August 2012.
    * Improve operation under MSWindows: substitute "\" for "/" for
      directory separator in command lines, deal consistently with
      directory separator, which can be both "\" and "/".
    * Correct some bugs that interfered with use of auxiliary directory
      and output directory for files generated by (pdf)latex, especially
      with MiKTeX.
    * Fix problems caused because in the log and fls files MiKTeX writes
      absolute path for many filenames at and below current directory, and
      is inconsistent in its use of "/" vs. "\" as directory separator.
    * Add $dvipdf_silent_switch configuration variable.
    * Improve handling of errors in (pdf)latex; previously latexmk would
      give up processing in some situations continuing is correct.
    * Documentation corrections/improvements.
    * Reduce number of warnings in silent operation.
  - 4.31 dated 30 March 2012.
    * Implement most options allowed by latex and pdflatex.
    * Add -M -MP and -MF options, like gcc.
    * Recorder option is now on by default.
    * Add -latexoption=... option to latexmk.
    * Add -xelatex option for use of xelatex.
    * Change OS-X default for pdf previewer command to open.
    * Command specification string can start with "include routine" to
      invoke a Perl subroutine instead of an external cmd.
    * Viewers are detached by default. (The start keyword is now normally
      superfluous in command specifications.)
    * Keyword nostart added in command specification.
    * Add configuration variables $compiling_cmd, $success_cmd,
      $failure_cmd. These specify external commands (if any) to be
      executed during latexmk's continuous preview mode at the following
      points: $compiling_cmd at the start of compilation, $success_cmd at
      the end of a successful compilation, and $failure_cmd at the end of
      an unsuccessful compilation. They can be used, for example, to show
      the progress of compilation by setting the titles of editor and/or
      previewer windows.
    * If aux and/or output directories are specified but don't exist, make
      them.
    * Remove excessive repetition of tests for changes of source files
      (improves performance of latexmk in some situations).
    * Documentation improvements.
    * Minor bug corrections.
  - 4.30a dated 9 December 2011.
    * Fix use of bibtex so that it works correctly when $aux_dir and/or
      $out_dir are set.
    * Use OS-dependent search path separator when when manipulating
      TEXINPUTS, etc. Then use of -output-directory and -aux-directory
      options should work correctly on MSWin systems.
    * Documentation of $search_path_separator variable.
    * Correct some bugs in v. 4.30 that manifested themselves under MSWin
      especially with Cygwin.
  - 4.29a dated 7 December 2011.
    * Latexmk now works with the feynmp package and mpost, provided a
      suitable custom dependency is defined. (See the example latexmkrc
      fragment mpost_latexmkrc in the example_rcfiles directory in the
      latexmk distribution.)
    * If output directory is set, arrange that dvips can find files there.
    * In searching for cus-deps that can make a missing file, look in
      $out_dir.
  - 4.28c dated 1 December 2011.
    * When biber doesn't find the bib file, latexmk treats this as a
      warning rather than a fatal error, so further processing can
      continue normally.
    * Latexmk now parses correctly error messages from biber v. 0.9.7.
  - 4.28a dated 28 November 2011.
    * Correct handling of situations where some file(s) needed by bibtex
      (or biber) don't exist. Previously latexmk incorrectly stopped with
      an error message instead of continuing.
    * Correct duplicate invocations of dvipdf, ps2pdf
  - 4.27a dated 10 October 2011.
    * Deal with problem that making of ps or pdf file via a temporary file
      fails if the command making it has no %D placeholder
    * Add png to list of graphics extensions for pdflatex
    * Add -norc option that prevents auto reading of rc files.
    * Options -aux-directory -output-directory like those of (pdf)latex,
      to set the output directories of (pdf)latex. (-aux-directory is
      MiKTeX only). Corresponding configuration variables, and
      placeholders for command specification.
  - 4.26 dated 9 August 2011.
    * Make compatible with biber 0.9.4.
    * Fix some bugs in error reporting.
  - 4.25 dated 7 July 2011.
    * Fix to evade apparent cygwin bug that prevented system rc-file from
      being read.
    * Diagnostic for unreadable rc-file.
    * Add deps output file to target part of dependency information.
* debian/patches:
  - Refreshed
* debian/control:
  - Replaced gs-common by ghostscript as Suggested package Closes: #649700
* Previous changes by Antonio Ospite (4.24-1.2) Closes: #693126 and by
  Jari Aalto (4.24-1.1) Closes: #668926

8. By Matthieu Baerts on 2012-12-27

* debian/patches/rc-system-files.patch:
  - This file has a wrong name according to debian/patches/series

7. By Matthieu Baerts on 2012-12-27

Added debian/watch file

6. By Matthieu Baerts on 2012-12-27

* Non-maintainer upload.
* Remove deprecated dpatch and upgrade to packaging format "3.0 quilt".
* Update to Standards-Version to 3.9.3 and debhelper to 9.
* Add required build-arch and build-indep targets to rules file.
* Fix old-fsf-address-in-copyright-file (Lintian).
* Fix copyright-refers-to-symlink-license (Lintian).
* Fix capitalization-error-in-description LaTeX (Lintian).
* Fix no-homepage-field (Lintian).

=== modified file 'CHANGES'
--- CHANGES	2011-06-11 22:09:09 +0000
+++ CHANGES	2012-12-28 00:31:23 +0000
@@ -257,3 +257,141 @@
     aren't in the current directory (by use of kpsewhich).  This was
     previously done for bibtex but not biber.
 
+From v. 4.24 to v. 4.25
+    Fix to evade apparent cygwin bug that prevented system
+       rc-file from being read.
+    Diagnostic for unreadable rc-file.
+    Add deps output file to target part of dependency information
+
+From v. 4.25 to v. 4.26
+    Make compatible with biber 0.9.4.
+    Fix some bugs in error reporting.
+
+From v. 4.26 to v. 4.27a
+    Deal with problem that making of ps or pdf file via a temporary
+       file fails if the command making it has no %D placeholder
+    Add png to list of graphics extensions for pdflatex
+    Add -norc option that prevents auto reading of rc files.
+    Options -aux-directory -output-directory like those of (pdf)latex, 
+       to set the output directories of (pdf)latex.  (-aux-directory
+       is MiKTeX only).  Corresponding configuration variables, and
+       placeholders for command specification.
+
+From v. 4.27a to 4.28
+    Correct handling of situations where some file(s) needed by bibtex
+       (or biber) don't exist.  Previously latexmk incorrectly stopped
+       with an error message instead of continuing.
+
+From v. 4.28 to 4.28a
+    Correct duplicate making of view file
+
+From v. 4.28a to 4.28c
+    When biber doesn't find the bib file, latexmk treats this as a
+       warning rather than a fatal error, so further processing
+       can continue normally.
+    Latexmk now parses correctly error messages from biber v. 0.9.7.
+
+From v. 4.28c to 4.29a
+    Latexmk now works with the feynmp package and mpost,
+       provided a suitable custom dependency is defined.  (See the
+       example latexmkrc fragment mpost_latexmkrc in the
+       example_rcfiles directory in the latexmk distribution.)
+    If output directory is set, arrange that dvips can find files
+      there.
+    In  searching for cus-deps that can make a missing file, look in
+      $out_dir.
+    Solves problem that sometimes dvips and dvipdf weren't run when
+      they should have been.  (The problem only arose with certain 
+      changes in eps files being made within a minute of the previous
+      run.)
+
+From v. 4.29a to 4.30a
+    Fix use of bibtex so that it works correctly when $aux_dir and/or
+       $out_dir are set.
+    Use OS-dependent search path separator when when manipulating
+       TEXINPUTS, etc. Then use of -output-directory and
+       -aux-directory options should work on MSWin systems.
+    Documentation of $search_path_separator variable.
+
+From v. 4.30a to 4.31
+    Add -M -MP and -MF options, like gcc.
+    Recorder option is now on by default.
+    Add options reproducing most options of (pdf)latex (list from both
+       TeXLive and MikTeX versions).  
+       Options NOT implemented by latexmk at all:
+           -ini and -initialize  since they refer to operations
+                                 not supported by latexmk
+           -includedirectory=dir its support needs extra code in
+                                 latexmk, not currently written
+      Options differently processed by latexmk:
+           -help
+           -version
+           -quiet
+      Options that are passed to (pdf)latex but that also have special
+      processing by latexmk
+           -aux-directory=dir
+           -output-directory=dir
+           -recorder
+    Add -latexoption=... option to latexmk
+    Add -xelatex option for use of xelatex
+    Change OS-X default for pdf previewer command to open
+    Command specification string can start with "include routine" to
+       invoke a Perl subroutine instead of an external cmd.
+    Viewers are detached by default.  (The start keyword is now normally
+      superfluous in command specifications.)
+    Keyword nostart added in command specification.
+    Add configuration variables $compiling_cmd, $success_cmd,
+      $failure_cmd.  These specify external commands (if any) to be
+      executed during latexmk's continuous preview mode at the
+      following points: $compiling_cmd at the start of compilation,
+      $success_cmd at the end of a successful compilation, and
+      $failure_cmd at the end of an unsuccessful compilation.  They
+      can be used, for example, to show the progress of compilation by
+      setting the titles of editor and/or previewer windows.
+    If aux and/or output directories are specified but don't exist,
+      make them.
+    Remove excessive repetition of tests for changes of source files
+      (improves performance of latexmk in some situations).
+    Documentation improvements.
+    Minor bug corrections.
+
+From v. 4.31 to 4.33a
+   Improve operation under MSWindows: substitute "\" for "/" for
+     directory separator in command lines, deal consistently with
+     directory separator, which can be both "\" and "/".
+   Correct some bugs that interfered with use of auxiliary directory
+     and output directory for files generated by (pdf)latex,
+     especially with MiKTeX.
+   Fix problems caused because in the log and fls files MiKTeX writes
+     absolute path for many filenames at and below current directory,
+     and is inconsistent in its use of "/" vs. "\" as directory
+     separator. 
+   Add $dvipdf_silent_switch configuration variable.
+   Improve handling of errors in (pdf)latex; previously latexmk would
+     give up processing in some situations continuing is correct.
+   Documentation corrections/improvements.
+   Reduce number of warnings in silent operation.
+   Cure slowness of v. 4.33 under Cygwin.
+
+From v. 4.33a to 4.33b
+   Documentation improvements.
+   Improve text displayed by using -showextraoptions option.
+
+From v. 4.33b to 4.33c
+   Correct infinite loop when maximum passes through latex/pdflatex
+      are exceeded
+
+From v. 4.33c to 4.34
+   Correct non-optimality that if (pdf)latex reads a file only after
+      it has been written in the same run, the file is not a true
+      source file, but nevertheless latexmk treats it as a source
+      file.  Thus changes in the file sometimes caused latexmk to make
+      unnecessary (but otherwise innocuous) extra runs of (pdflatex).
+
+From v. 4.34 to 4.35
+   Correct bug in parsing fls file from native MS-Windows LaTeX (e.g.,
+      MiKTeX) when latexmk is run under cygwin.  (The names of some
+      files used by latexmk incorrectly contained a CR character.)
+   Correct bug that when the --gg option is used, the rule database
+      from the old fdb file was used instead of being cleared.
+
 
=== modified file 'INSTALL'
--- INSTALL	2011-06-11 22:09:09 +0000
+++ INSTALL	2012-12-28 00:31:23 +0000
@@ -1,6 +1,6 @@
             INSTALLING latexmk
             ==================
-      (Version 4.24, 7 May 2011)
+      (Version 4.35, 11 November 2012)
 
             John Collins
             Physics Department
 
=== modified file 'README'
--- README	2011-06-11 22:09:09 +0000
+++ README	2012-12-28 00:31:23 +0000
@@ -1,5 +1,5 @@
-Latexmk, version 4.24, 7 May 2011
----------------------------------
+Latexmk, version 4.35, 11 November 2012
+---------------------------------------
 
 Latexmk completely automates the process of generating a LaTeX
 document.  Essentially, it is a highly specialized cousin of the
@@ -92,14 +92,17 @@
 
 John Collins
 ---------------------------- "latexmk -h" ----------------------------
-Latexmk 4.24: Automatic LaTeX document generation routine
+Latexmk 4.35: Automatic LaTeX document generation routine
 
 Usage: latexmk [latexmk_options] [filename ...]
 
   Latexmk_options:
-   -bibtex         - use bibtex when needed (default)
-   -bibtex-        - never use bibtex
-   -bibtex-cond    - use bibtex when needed, but only if the bib files exist
+   -aux-directory=dir or -auxdir=dir 
+                 - set name of directory for auxiliary files (aux, log)
+                 - Currently this only works with MiKTeX
+   -bibtex       - use bibtex when needed (default)
+   -bibtex-      - never use bibtex
+   -bibtex-cond  - use bibtex when needed, but only if the bib files exist
    -bm <message> - Print message across the page when converting to postscript
    -bi <intensity> - Set contrast or intensity of banner
    -bs <scale> - Set scale for banner
@@ -140,10 +143,17 @@
    -l-    - turn off -l
    -latex=<program> - set program used for latex.
                       (replace '<program>' by the program name)
+   -latexoption=<option> - add the given option to the (pdf)latex command
+   -M     - Show list of dependent files after processing
+   -MF file - Specifies name of file to receives list dependent files
+   -MP    - List of dependent files includes phony target for each source file.
    -new-viewer    - in -pvc mode, always start a new viewer
    -new-viewer-   - in -pvc mode, start a new viewer only if needed
    -nobibtex      - never use bibtex
    -nodependents  - Do not show list of dependent files after processing
+   -norc          - omit automatic reading of system, user and project rc files
+   -output-directory=dir or -outdir=dir
+                  - set name of directory for output files
    -pdf   - generate pdf by pdflatex
    -pdfdvi - generate pdf by dvipdf
    -pdflatex=<program> - set program used for pdflatex.
@@ -164,12 +174,17 @@
                 on force mode, so errors do not cause latexmk to stop.)
             (Side effect: turn off ordinary preview mode.)
    -pvc-  - turn off -pvc
+   -quiet    - silence progress messages from called programs
    -r <file> - Read custom RC file
+               (N.B. This file could override options specified earlier
+               on the command line.)
    -recorder - Use -recorder option for (pdf)latex
                (to give list of input and output files)
    -recorder- - Do not use -recorder option for (pdf)latex
    -rules    - Show list of rules after processing
    -rules-   - Do not show list of rules after processing
+   -showextraoptions  - Show other allowed options that are simply passed
+               as is to latex and pdflatex
    -silent   - silence progress messages from called programs
    -time     - show CPU time used
    -time-    - don't show CPU time used
@@ -183,11 +198,15 @@
    -view=none    - no viewer is used
    -view=ps      - viewer is for ps
    -view=pdf     - viewer is for pdf
+   -xelatex      - use xelatex for processing files to pdf
+
    filename = the root filename of LaTeX document
 
 -p, -pv and -pvc are mutually exclusive
 -h, -c and -C override all other options.
 -pv and -pvc require one and only one filename specified
 All options can be introduced by '-' or '--'.  (E.g., --help or -help.)
-Contents of RC file specified by -r overrides options specified
-  before the -r option on the command line
+ 
+In addition, latexmk recognizes many other options that are passed to
+latex and/or pdflatex without interpretation by latexmk.  Run latexmk
+with the option -showextraoptions to see a list of these
 
=== modified file 'debian/changelog'
--- debian/changelog	2011-06-11 22:09:09 +0000
+++ debian/changelog	2012-12-28 00:31:23 +0000
@@ -1,3 +1,145 @@
+latexmk (1:4.35-0ubuntu1) raring; urgency=low
+
+  * New upstream release. (LP: #1094164)
+  * Upstream ChangeLog:
+    - 4.35 dated 11 November 2012.
+      * Corrects bug that fls file is incorrectly parsed when using a
+        combination of cygwin and a native MS-Windows TeX program.
+      * Corrects bug that old dependency information was retained when using
+        the --gg option. 
+    - 4.34 dated 1 October 2012.
+      * Corrects non-optimality that latexmk may do extra runs of (pdf)latex
+        when a file is read and written during a run of (pdf)latex, but the
+        file is only read after being written. 
+    - 4.33c dated 19 August 2012.
+      * Corrects infinite loop in error messages when the maximum number of
+        passes through latex/pdflatex is exceeded. 
+    - 4.33b dated 12 August 2012.
+      * Documentation improvements, including documentation of the many
+        options for the (pdf)latex programs that are supported by latexmk. 
+    - 4.33a dated 8 August 2012.
+      * Fix slowness of v. 4.33 under Cygwin. 
+    - 4.33 dated 6 August 2012.
+      * Improve operation under MSWindows: substitute "\" for "/" for
+        directory separator in command lines, deal consistently with
+        directory separator, which can be both "\" and "/".
+      * Correct some bugs that interfered with use of auxiliary directory
+        and output directory for files generated by (pdf)latex, especially
+        with MiKTeX.
+      * Fix problems caused because in the log and fls files MiKTeX writes
+        absolute path for many filenames at and below current directory, and
+        is inconsistent in its use of "/" vs. "\" as directory separator.
+      * Add $dvipdf_silent_switch configuration variable.
+      * Improve handling of errors in (pdf)latex; previously latexmk would
+        give up processing in some situations continuing is correct.
+      * Documentation corrections/improvements.
+      * Reduce number of warnings in silent operation. 
+    - 4.31 dated 30 March 2012.
+      * Implement most options allowed by latex and pdflatex.
+      * Add -M -MP and -MF options, like gcc.
+      * Recorder option is now on by default.
+      * Add -latexoption=... option to latexmk.
+      * Add -xelatex option for use of xelatex.
+      * Change OS-X default for pdf previewer command to open.
+      * Command specification string can start with "include routine" to
+        invoke a Perl subroutine instead of an external cmd.
+      * Viewers are detached by default. (The start keyword is now normally
+        superfluous in command specifications.)
+      * Keyword nostart added in command specification.
+      * Add configuration variables $compiling_cmd, $success_cmd,
+        $failure_cmd. These specify external commands (if any) to be
+        executed during latexmk's continuous preview mode at the following
+        points: $compiling_cmd at the start of compilation, $success_cmd at
+        the end of a successful compilation, and $failure_cmd at the end of
+        an unsuccessful compilation. They can be used, for example, to show
+        the progress of compilation by setting the titles of editor and/or
+        previewer windows.
+      * If aux and/or output directories are specified but don't exist, make
+        them.
+      * Remove excessive repetition of tests for changes of source files
+        (improves performance of latexmk in some situations).
+      * Documentation improvements.
+      * Minor bug corrections. 
+    - 4.30a dated 9 December 2011.
+      * Fix use of bibtex so that it works correctly when $aux_dir and/or
+        $out_dir are set.
+      * Use OS-dependent search path separator when when manipulating
+        TEXINPUTS, etc. Then use of -output-directory and -aux-directory
+        options should work correctly on MSWin systems.
+      * Documentation of $search_path_separator variable.
+      * Correct some bugs in v. 4.30 that manifested themselves under MSWin
+        especially with Cygwin. 
+    - 4.29a dated 7 December 2011.
+      * Latexmk now works with the feynmp package and mpost, provided a
+        suitable custom dependency is defined. (See the example latexmkrc
+        fragment mpost_latexmkrc in the example_rcfiles directory in the
+        latexmk distribution.)
+      * If output directory is set, arrange that dvips can find files there.
+      * In searching for cus-deps that can make a missing file, look in
+        $out_dir. 
+    - 4.28c dated 1 December 2011.
+      * When biber doesn't find the bib file, latexmk treats this as a
+        warning rather than a fatal error, so further processing can
+        continue normally.
+      * Latexmk now parses correctly error messages from biber v. 0.9.7. 
+    - 4.28a dated 28 November 2011.
+      * Correct handling of situations where some file(s) needed by bibtex
+        (or biber) don't exist. Previously latexmk incorrectly stopped with
+        an error message instead of continuing.
+      * Correct duplicate invocations of dvipdf, ps2pdf 
+    - 4.27a dated 10 October 2011.
+      * Deal with problem that making of ps or pdf file via a temporary file
+        fails if the command making it has no %D placeholder
+      * Add png to list of graphics extensions for pdflatex
+      * Add -norc option that prevents auto reading of rc files.
+      * Options -aux-directory -output-directory like those of (pdf)latex,
+        to set the output directories of (pdf)latex. (-aux-directory is
+        MiKTeX only). Corresponding configuration variables, and
+        placeholders for command specification. 
+    - 4.26 dated 9 August 2011.
+      * Make compatible with biber 0.9.4.
+      * Fix some bugs in error reporting. 
+    - 4.25 dated 7 July 2011.
+      * Fix to evade apparent cygwin bug that prevented system rc-file from
+        being read.
+      * Diagnostic for unreadable rc-file.
+      * Add deps output file to target part of dependency information. 
+  * debian/patches:
+    - Refreshed
+  * debian/control:
+    - Replaced gs-common by ghostscript as Suggested package Closes: #649700
+  * Previous changes by Antonio Ospite (4.24-1.2) Closes: #693126 and by
+    Jari Aalto (4.24-1.1) Closes: #668926
+
+ -- Matthieu Baerts (matttbe) <[e-mail]>  Fri, 28 Dec 2012 00:24:43 +0100
+
+latexmk (1:4.24-1.2ubuntu1) raring; urgency=low
+
+  * debian/patches/rc-system-files.patch:
+    - This file has a wrong name according to debian/patches/series
+
+ -- Matthieu Baerts (matttbe) <[e-mail]>  Thu, 27 Dec 2012 17:45:42 +0100
+
+latexmk (1:4.24-1.2) unstable; urgency=low
+
+  [ Antonio Ospite ]
+  * Added debian/watch file
+
+ -- Matthieu Baerts (matttbe) <[e-mail]>  Thu, 27 Dec 2012 17:15:34 +0100
+
+latexmk (1:4.24-1.1) unstable; urgency=low
+
+  * Non-maintainer upload.
+  * Remove deprecated dpatch and upgrade to packaging format "3.0 quilt".
+  * Update to Standards-Version to 3.9.3 and debhelper to 9.
+  * Add required build-arch and build-indep targets to rules file.
+  * Fix old-fsf-address-in-copyright-file (Lintian).
+  * Fix copyright-refers-to-symlink-license (Lintian).
+  * Fix capitalization-error-in-description LaTeX (Lintian).
+  * Fix no-homepage-field (Lintian).
+
+ -- Jari Aalto <[e-mail]>  Sun, 15 Apr 2012 20:25:54 +0300
+
 latexmk (1:4.24-1) unstable; urgency=low
 
   * New upstream release (Closes: #564199).
 
=== modified file 'debian/compat'
--- debian/compat	2006-06-12 00:43:25 +0000
+++ debian/compat	2012-12-28 00:31:23 +0000
@@ -1,1 +1,1 @@
-5
+9
 
=== modified file 'debian/control'
--- debian/control	2011-06-11 22:09:09 +0000
+++ debian/control	2012-12-28 00:31:23 +0000
@@ -1,19 +1,21 @@
 Source: latexmk
 Section: tex
 Priority: optional
-Build-Depends: debhelper (>= 5.0.0), dpatch
-Maintainer: OHURA Makoto <[e-mail]>
-Standards-Version: 3.9.2
+Build-Depends: debhelper (>= 9)
+Maintainer: Ubuntu Developers <[e-mail]>
+XSBC-Original-Maintainer: OHURA Makoto <[e-mail]>
+Standards-Version: 3.9.3
+Homepage: http://www.phys.psu.edu/~collins/software/latexmk-jcc
 
 Package: latexmk
 Architecture: all
 Depends: perl, texlive-latex-base, ${misc:Depends}
-Suggests: gs-common
+Suggests: ghostscript
 Recommends: xpdf-reader | pdf-viewer, gv | postscript-viewer
 Description: Perl script for running LaTeX the correct number of times
  Latexmk runs LaTeX the correct number of times to resolve cross references,
  etc; it also runs auxiliary programs (bibtex, makeindex if necessary, and
  dvips and/or a previewer as requested). It has a number of other useful
- capabilities, for example to start a previewer and then run latex whenever the
+ capabilities, for example to start a previewer and then run LaTeX whenever the
  source files are updated, so that the previewer gives an up-to-date view of
  the document.
 
=== modified file 'debian/copyright'
--- debian/copyright	2006-06-12 00:43:25 +0000
+++ debian/copyright	2012-12-28 00:31:23 +0000
@@ -28,10 +28,5 @@
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
-
-
 On Debian GNU/Linux systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
+Public License can be found in `/usr/share/common-licenses/GPL-2'.
 
=== removed file 'debian/patches/00list'
--- debian/patches/00list	2006-06-12 00:43:25 +0000
+++ debian/patches/00list	1970-01-01 00:00:00 +0000
@@ -1,1 +0,0 @@
-rc_system_files
 
=== renamed file 'debian/patches/rc_system_files.dpatch' => 'debian/patches/rc-system-files.patch'
--- debian/patches/rc_system_files.dpatch	2006-06-12 00:43:25 +0000
+++ debian/patches/rc-system-files.patch	2012-12-28 00:31:23 +0000
@@ -1,14 +1,12 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## rc_system_files.dpatch by Florian Ragwitz <[e-mail]>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: add /etc/LatexMk to @rc_system_files
-
-@DPATCH@
-
---- latexmk-307a.orig/latexmk.pl	2006-06-12 01:39:17.959196512 +0200
-+++ latexmk-307a/latexmk.pl	2006-06-12 01:39:56.378355912 +0200
-@@ -537,7 +537,8 @@
+From: Florian Ragwitz <[e-mail]>
+Subject: add /etc/LatexMk to @rc_system_files
+
+
+Index: latexmk/latexmk.pl
+===================================================================
+--- latexmk.orig/latexmk.pl	2012-12-27 17:50:00.211349000 +0100
++++ latexmk/latexmk.pl	2012-12-27 17:55:02.858109192 +0100
+@@ -895,7 +895,8 @@
      ## /usr/local/lib/latexmk/LatexMk is put in the list for
      ## compatibility with older versions of latexmk.
      @rc_system_files = 
 
=== added file 'debian/patches/series'
--- debian/patches/series	1970-01-01 00:00:00 +0000
+++ debian/patches/series	2012-12-28 00:31:23 +0000
@@ -0,0 +1,1 @@
+rc-system-files.patch
 
=== modified file 'debian/rules'
--- debian/rules	2006-06-12 00:43:25 +0000
+++ debian/rules	2012-12-28 00:31:23 +0000
@@ -1,28 +1,21 @@
 #!/usr/bin/make -f
 
-clean: clean1 unpatch
-clean1:
+clean:
 	dh_testdir
 	dh_testroot
 	rm -f install-stamp
 	dh_clean
 
-build: patch
-
-patch: patch-stamp
-patch-stamp:
-	dpatch apply-all
-	touch patch-stamp
-
-unpatch:
-	dpatch deapply-all
-	rm -rf patch-stamp debian/patched
+build-arch: build
+build-indep: build
+
+build:
 
 install: install-stamp
 install-stamp:
 	dh_testdir
 	dh_testroot
-	dh_clean -k
+	dh_prep
 	dh_installdirs
 	install -m755 $(CURDIR)/latexmk.pl    $(CURDIR)/debian/latexmk/usr/bin/latexmk
 	install -m644 $(CURDIR)/debian/config $(CURDIR)/debian/latexmk/etc/LatexMk
@@ -45,4 +38,4 @@
 
 binary: binary-arch binary-indep
 
-.PHONY: clean build install binary-indep binary-arch binary patch unpatch
+.PHONY: clean build install binary-indep binary-arch binary
 
=== added directory 'debian/source'
=== added file 'debian/source/format'
--- debian/source/format	1970-01-01 00:00:00 +0000
+++ debian/source/format	2012-12-28 00:31:23 +0000
@@ -0,0 +1,1 @@
+3.0 (quilt)
 
=== added file 'debian/watch'
--- debian/watch	1970-01-01 00:00:00 +0000
+++ debian/watch	2012-12-28 00:31:23 +0000
@@ -0,0 +1,8 @@
+version=3
+
+# In the pattern below the first digit is isolated so to have a dotted
+# version number in the debian packages, the upstream uses this dotted
+# form in the changelog but removes the dot in the file names.
+http://www.phys.psu.edu/~collins/software/latexmk-jcc/versions.html \
+  latexmk-([\d])([\d]+[a-z]*).zip \
+  debian uupdate
 
=== modified file 'example_rcfiles/README'
--- example_rcfiles/README	2011-06-11 22:09:09 +0000
+++ example_rcfiles/README	2012-12-28 00:31:23 +0000
@@ -20,3 +20,16 @@
    examples.  (The file Latexmk321jTeXShop.zip is the one you want.)
    It shows how to use glossaries, epstopdf, pdftricks and pst-pdf.
 
+4. I have generally arranged for filenames to be quoted on command
+   lines, e.g., 
+
+       system( "makeindex -o \"$_[0].lnd\" \"$_[0].ldx\"" );
+
+   In many cases the quotes may be omitted, as in 
+
+       system( "makeindex -o $_[0].lnd $_[0].ldx" );
+
+   But it is preferable to leave the quotes in, since they provide
+   safety against special characters in filenames.  The double quotes
+   appear not to cause problems in all situations that I have tried.
+
 
=== added file 'example_rcfiles/Sweave_latexmkrc'
--- example_rcfiles/Sweave_latexmkrc	1970-01-01 00:00:00 +0000
+++ example_rcfiles/Sweave_latexmkrc	2012-12-28 00:31:23 +0000
@@ -0,0 +1,57 @@
+# This is to allow the use of Sweave with latexmk, and in addition to
+#    make synctex work properly with it.  
+# SEE THE IMPORTANT NOTES below.
+#
+# Sweave (http://www.stat.uni-muenchen.de/~leisch/Sweave/) is a tool
+# that allows to embed the R code for complete data analyses in latex
+# documents.  The user edits a file with an extension like .Rnw, and
+# the .tex file is generated from this.
+#
+# Four problems are solved by the code below:
+# 1. Generate the .tex file automatically.
+# 2. Arrange not to re-run unmodified chunks of R code.  (A pure
+#    optimization.)
+# 3. Fix the execution environment for (pdf)latex.
+# 4. Deal with synctex: If the user wants to use synctex
+#    (www.tug.org/TUGboat/tb29-3/tb93laurens.pdf) to synchronize the
+#    pdf file with the source file, by default synctex does the
+#    synchronization with the generated .tex file, not the original 
+#    source file.  Postprocessing of the .synctex.gz file is necessary
+#    to fix this.
+#
+# The following version was worked out and  tested by a user (thanks
+# to Brian Beitzel) on MSWindows.  It will need at least one change to
+# work on UNIX-like operating systems (which include Linux and OS-X).
+
+# N.B. ===> IMPORTANT NOTES <===
+#
+# 1. The patchDVI package for R needs to be installed from R-Forge, as
+#    follows:
+#
+#  install.packages("patchDVI", repos="http://R-Forge.R-project.org")
+#
+# 2. In all Sweave (.Rnw) documents, the following lines must be included:
+#
+#         \usepackage{Sweave}
+#         \SweaveOpts{concordance=TRUE}
+
+
+# Fix the pdflatex command to run Sweave first, and to postprocess the
+#  .synctex.gz file:
+# !!!!! THIS IS THE VERSION FOR MS-WINDOWS, with && as a command
+# separator
+$pdflatex = "cmd /c "
+       . "Rscript -e \"library(cacheSweave); setCacheDir(getwd()); "
+       . "Sweave('%S', driver=cacheSweaveDriver)\""
+       . " && R CMD pdflatex -interaction=nonstopmode -synctex=1 %O %B.tex"
+       . " && Rscript -e "
+       . "\"library('patchDVI');patchSynctex('%B.synctex.gz')\"";
+#
+# !!!TO FIX THIS FOR Linux/OS-X/UNIX, try uncommenting the following:
+#  (this version hasn't been tested).
+#$pdflatex = "Rscript -e \"library(cacheSweave); setCacheDir(getwd()); "
+#       . "Sweave('%S', driver=cacheSweaveDriver)\""
+#       . " ; R CMD pdflatex -interaction=nonstopmode -synctex=1 %O %B.tex"
+#       . " ; Rscript -e "
+#       . "\"library('patchDVI');patchSynctex('%B.synctex.gz')\"";
+
 
=== added file 'example_rcfiles/TeX4ht-latexmkrc'
--- example_rcfiles/TeX4ht-latexmkrc	1970-01-01 00:00:00 +0000
+++ example_rcfiles/TeX4ht-latexmkrc	2012-12-28 00:31:23 +0000
@@ -0,0 +1,33 @@
+# Sometime in the future, latexmk will directly support the use of
+# TeX4ht to obtain html from tex.  Meanwhile, here is how to use
+# latexmk with TeX4ht.  There is a script htlatex supplied by the
+# TeX4ht package: It simply runs latex a fixed number of times and
+# then the programs tex4ht and t4ht.  To use latexmk to get optimal
+# processing use the following instructions (under UNIX-like operating
+# systems, e.g., OS-X and linux):
+#
+#  1. Put the scripts htlatexonly and myhtlatex2 somewhere in the PATH
+#     for executables (and make sure they have excutable permissions
+#     set).
+#  2. Set up an initialization file for latexmk like this one.
+#
+#  3. To process file.tex to make file.html, run
+#
+#             myhtlatex2 file
+#
+
+# Since these instructions use scripts that are UNIX shell scripts,
+# the instructions work as written for UNIX-like operating
+# systems. Users of other operating systems will have to adjust them
+# and modify the scripts suitably.
+
+
+warn "latexmkrc for htlatex\n";
+
+$dvi_mode = 1;
+$pdf_mode = 0;
+$quote_filenames = 0;
+$latex = 'htlatexonly %S';
+
+$clean_ext .= ' 4ct 4tc idv lg tmp xref';
+$clean_full_ext .= ' css html';
 
=== modified file 'example_rcfiles/asymptote_latexmkrc'
--- example_rcfiles/asymptote_latexmkrc	2011-06-11 22:09:09 +0000
+++ example_rcfiles/asymptote_latexmkrc	2012-12-28 00:31:23 +0000
@@ -21,7 +21,7 @@
 
 # The following lines are taken from the documentation for V. 2.03 of
 # asymptote:
-sub asy {return system("asy '$_[0]'");}
+sub asy {return system("asy \"$_[0]\"");}
 add_cus_dep("asy","eps",0,"asy");
 add_cus_dep("asy","pdf",0,"asy");
 add_cus_dep("asy","tex",0,"asy");
 
=== modified file 'example_rcfiles/glossary_latexmkrc'
--- example_rcfiles/glossary_latexmkrc	2011-06-11 22:09:09 +0000
+++ example_rcfiles/glossary_latexmkrc	2012-12-28 00:31:23 +0000
@@ -10,18 +10,18 @@
 
 # 1. For glossaries using glossary package
 
-add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
+add_cus_dep( 'glo', 'gls', 0, 'makeglo2gls' );
 sub makeglo2gls {
-    system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo");
+    system("makeindex -s \"$_[0].ist\" -t \"$_[0].glg\" -o \"$_[0].gls\" \"$_[0].glo\"" );
 }
 
 
 
 # 2. For acronyms using glossary package:
 
-add_cus_dep('acr', 'acn', 0, 'makeacr2acn');
+add_cus_dep( 'acr', 'acn', 0, 'makeacr2acn' );
 sub makeacr2acn {
-    system("makeindex -s '$_[0]'.ist -t '$_[0]'.alg -o '$_[0]'.acn '$_[0]'.acr");
+    system( "makeindex -s \"$_[0].ist\" -t \"$_[0].alg\" -o \"$_[0].acn\" \"$_[0].acr\"" );
 }
 
 
@@ -31,8 +31,8 @@
 # 4. If you use the glossaries package and have the makeglossaries
 #    script installed, then you can do something simpler:
 
-   add_cus_dep('glo', 'gls', 0, 'makeglossaries');
+   add_cus_dep( 'glo', 'gls', 0, 'makeglossaries' );
    sub makeglossaries {
-      system("makeglossaries $_[0]");
+      system( "makeglossaries \"$_[0]\"" );
    }
 
 
=== added file 'example_rcfiles/mpost_latexmkrc'
--- example_rcfiles/mpost_latexmkrc	1970-01-01 00:00:00 +0000
+++ example_rcfiles/mpost_latexmkrc	2012-12-28 00:31:23 +0000
@@ -0,0 +1,26 @@
+# This shows how to use mpost, as used by the feynmp package.
+# The feynmp package writes files with extension .mp, e.g., foo.mp,
+# and these are to be converted by mpost to make postscript files,
+# e.g., foo.1, which are later read in by dvips.
+#
+# A more complicated custom dependency is needed than normal, because:
+# if the output directory ($out_dir) or the auxiliary directory
+# ($out_dir) is set, mpost doesn't put its output in the correct
+# place.
+
+add_cus_dep( 'mp', '1', 0, 'mpost' );
+
+
+sub mpost {
+    my $file = $_[0];
+    my ($name, $path) =  fileparse( $file );
+    my $return = system "mpost \"$file\"";
+        # Fix the problem that mpost puts its output and log files
+        # in the current directory, not in the auxiliary directory
+        # (which is often the same as the output directory):
+    if ( ($path ne '') && ($path ne '.\\') && ($path ne './') ) {
+        foreach ( "$name.1", "$name.log" ) { move $_, $aux_dir; }
+    }
+    return $return;
+}
+
 
=== modified file 'example_rcfiles/pdflatexmkrc'
--- example_rcfiles/pdflatexmkrc	2010-03-14 17:10:22 +0000
+++ example_rcfiles/pdflatexmkrc	2012-12-28 00:31:23 +0000
@@ -6,72 +6,72 @@
 
 # Custom dependency for glossary/glossaries package
 # if you make custom glossaries you may have to add items to the @cus_dep_list and corresponding sub-routines
-add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
-		sub makeglo2gls {
-				system("makeindex -s $_[0].ist -t $_[0].glg -o $_[0].gls $_[0].glo");
-		}
+add_cus_dep( 'glo', 'gls', 0, 'makeglo2gls' );
+sub makeglo2gls {
+    system( "makeindex -s \"$_[0].ist\" -t \"$_[0].glg\" -o \"$_[0].gls\" \"$_[0].glo\"" );
+}
 # The glossaries package, with the [acronym] option, produces a .acn file when processed with (xe/pdf)latex and
 # then makeindex to process the .acn into .acr and finally runs of (xe/pdf)latex to read in the .acr file. Unfortunately
 # the glossary package does just the reverse; i.e. (xe/pdf)latex processing produces a .acr files and makeindex then
 # is used to convert the .acr file to a .acn file which is then ... . This dependency assumes the glossaries package.
-add_cus_dep('acn', 'acr', 0, 'makeacn2acr');
-		sub makeacn2acr {
-				system("makeindex -s $_[0].ist -t $_[0].alg -o $_[0].acr $_[0].acn");
-		}
+add_cus_dep( 'acn', 'acr', 0, 'makeacn2acr' );
+sub makeacn2acr {
+    system( "makeindex -s \"$_[0].ist\" -t \"$_[0].alg\" -o \"$_[0].acr\" \"$_[0].acn\"" );
+}
 # for glossary package (Sigh...) --- they can co-exist!		
-add_cus_dep('acr', 'acn', 0, 'makeacr2acn');
-		sub makeacr2acn {
-				system("makeindex -s $_[0].ist -t $_[0].alg -o $_[0].acn $_[0].acr");
-		}
+add_cus_dep( 'acr', 'acn', 0, 'makeacr2acn' );
+sub makeacr2acn {
+    system( "makeindex -s \"$_[0].ist\" -t \"$_[0].alg\" -o \"$_[0].acn\" \"$_[0].acr\"" );
+}
 # example of an added custom glossary type that is used in some of the glossary/glossaries example files:
 # this is for the new glossary type command \newglossary[nlg]{notation}{not}{ntn}{Notation} from the glossaries package
 # NOTE: the glossary package uses a very different command: the <in-ext> and <out-ext>
 # are reversed in the calling sequence :-(
-add_cus_dep('ntn', 'not', 0, 'makentn2not');
-		sub makentn2not {
-				system("makeindex -s $_[0].ist -t $_[0].nlg -o $_[0].not $_[0].ntn");
-		}
+add_cus_dep( 'ntn', 'not', 0, 'makentn2not' );
+sub makentn2not {
+    system("makeindex -s \"$_[0].ist\" -t \"$_[0].nlg\" -o \"$_[0].not\" \"$_[0].ntn\"" );
+}
 # for the	glossary package (Sigh...) --- they can co-exist!
-add_cus_dep('not', 'ntn', 0, 'makenot2ntn');
-		sub makenot2ntn {
-				system("makeindex -s $_[0].ist -t $_[0].nlg -o $_[0].ntn $_[0].not");
-		}
+add_cus_dep( 'not', 'ntn', 0, 'makenot2ntn' );
+sub makenot2ntn {
+    system("makeindex -s \"$_[0].ist\" -t \"$_[0].nlg\" -o \"$_[0].ntn\" \"$_[0].not\"" );
+}
 
 # dependencies for custom indexes using the index package
 # examples for sample.tex for index package:
- add_cus_dep('adx', 'and', 0, 'makeadx2and');
- 		sub makeadx2and {
- 				system("makeindex -o $_[0].and $_[0].adx");
- 		}
- add_cus_dep('ndx', 'nnd', 0, 'makendx2nnd');
- 		sub makendx2nnd {
- 				system("makeindex -o $_[0].nnd $_[0].ndx");
- 		}
- add_cus_dep('ldx', 'lnd', 0, 'makeldx2lnd');
- 		sub makeldx2lnd {
- 				system("makeindex -o $_[0].lnd $_[0].ldx");
- 		}
+ add_cus_dep( 'adx', 'and', 0, 'makeadx2and' );
+sub makeadx2and {
+    system( "makeindex -o \"$_[0].and\" \"$_[0].adx\"" );
+}
+add_cus_dep( 'ndx', 'nnd', 0, 'makendx2nnd' );
+sub makendx2nnd {
+    system( "makeindex -o \"$_[0].nnd\" \"$_[0].ndx\"" );
+}
+add_cus_dep( 'ldx', 'lnd', 0, 'makeldx2lnd' );
+sub makeldx2lnd {
+    system( "makeindex -o \"$_[0].lnd\" \"$_[0].ldx\"" );
+}
 
 # Custom dependency and function for nomencl package
-add_cus_dep('nlo', 'nls', 0, 'makenlo2nls');
-		sub makenlo2nls {
-				system("makeindex -s nomencl.ist -o $_[0].nls $_[0].nlo");
-		}
+add_cus_dep( 'nlo', 'nls', 0, 'makenlo2nls' );
+sub makenlo2nls {
+    system( "makeindex -s nomencl.ist -o \"$_[0].nls\" \"$_[0].nlo\"" );
+}
 
 # Custom dependency and function(s) for epstopdf package
 
 # FOR USERS OF epstopf v1.4 and before: should also work with v1.5 and later
 # note: you may get extras runs if you use the .eps extension in the \includgraphics command
 # deletes an outdated pdf-image, and triggers a pdflatex-run
-add_cus_dep('eps', 'pdf', 0, 'cus_dep_delete_dest');
+add_cus_dep( 'eps', 'pdf', 0, 'cus_dep_delete_dest' );
 
 # FOR USERS OF epstopdf v1.5 and later only:
 # load it as \usepackage[update,prepend]{epstopdf}
 # detects an outdated pdf-image, and triggers a pdflatex-run
-#add_cus_dep('eps', 'pdf', 0, 'cus_dep_require_primary_run');
+#add_cus_dep( 'eps', 'pdf', 0, 'cus_dep_require_primary_run' );
 
 # Custom dependecy to convert tif to png
-add_cus_dep('tif', 'png', 0, 'maketif2png');
-		sub maketif2png {
-				system("convert $_[0].tif $_[0].png");
-		}
+add_cus_dep( 'tif', 'png', 0, 'maketif2png' );
+sub maketif2png {
+    system( "convert \"$_[0].tif\" \"$_[0].png\"" );
+}
 
=== modified file 'example_rcfiles/sagetex_latexmkrc'
--- example_rcfiles/sagetex_latexmkrc	2011-06-11 22:09:09 +0000
+++ example_rcfiles/sagetex_latexmkrc	2012-12-28 00:31:23 +0000
@@ -14,8 +14,8 @@
 # changed. 
 
 
-add_cus_dep('sage', 'sout', 0, 'makesout');
+add_cus_dep( 'sage', 'sout', 0, 'makesout' );
 $hash_calc_ignore_pattern{'sage'} = '^( _st_.goboom|print .SageT)';
 sub makesout {
-   system("sage '$_[0].sage'");
+   system( "sage \"$_[0].sage\"" );
 }
 \ No newline at end of file
 
=== added file 'example_rcfiles/sweave_latexmkrc'
--- example_rcfiles/sweave_latexmkrc	1970-01-01 00:00:00 +0000
+++ example_rcfiles/sweave_latexmkrc	2012-12-28 00:31:23 +0000
@@ -0,0 +1,57 @@
+# This is to allow the use of Sweave with latexmk, and in addition to
+#    make synctex work properly with it.  
+# SEE THE IMPORTANT NOTES below.
+#
+# Sweave (http://www.stat.uni-muenchen.de/~leisch/Sweave/) is a tool
+# that allows to embed the R code for complete data analyses in latex
+# documents.  The user edits a file with an extension like .Rnw, and
+# the .tex file is generated from this.
+#
+# Four problems are solved by the code below:
+# 1. Generate the .tex file automatically.
+# 2. Arrange not to re-run unmodified chunks of R code.  (A pure
+#    optimization.)
+# 3. Fix the execution environment for (pdf)latex.
+# 4. Deal with synctex: If the user wants to use synctex
+#    (www.tug.org/TUGboat/tb29-3/tb93laurens.pdf) to synchronize the
+#    pdf file with the source file, by default synctex does the
+#    synchronization with the generated .tex file, not the original 
+#    source file.  Postprocessing of the .synctex.gz file is necessary
+#    to fix this.
+#
+# The following version was worked out and  tested by a user (thanks
+# to Brian Beitzel) on MSWindows.  It will need at least one change to
+# work on UNIX-like operating systems (which include Linux and OS-X).
+
+# N.B. ===> IMPORTANT NOTES <===
+#
+# 1. The patchDVI package for R needs to be installed from R-Forge, as
+#    follows:
+#
+#  install.packages("patchDVI", repos="http://R-Forge.R-project.org")
+#
+# 2. In all Sweave (.Rnw) documents, the following lines must be included:
+#
+#         \usepackage{Sweave}
+#         \SweaveOpts{concordance=TRUE}
+
+
+# Fix the pdflatex command to run Sweave first, and to postprocess the
+#  .synctex.gz file:
+# !!!!! THIS IS THE VERSION FOR MS-WINDOWS, with && as a command
+# separator
+$pdflatex = "cmd /c "
+       . "Rscript -e \"library(cacheSweave); setCacheDir(getwd()); "
+       . "Sweave('%S', driver=cacheSweaveDriver)\""
+       . " && R CMD pdflatex -interaction=nonstopmode -synctex=1 %O %B.tex"
+       . " && Rscript -e "
+       . "\"library('patchDVI');patchSynctex('%B.synctex.gz')\"";
+#
+# !!!TO FIX THIS FOR Linux/OS-X/UNIX, try uncommenting the following:
+#  (this version hasn't been tested).
+#$pdflatex = "Rscript -e \"library(cacheSweave); setCacheDir(getwd()); "
+#       . "Sweave('%S', driver=cacheSweaveDriver)\""
+#       . " ; R CMD pdflatex -interaction=nonstopmode -synctex=1 %O %B.tex"
+#       . " ; Rscript -e "
+#       . "\"library('patchDVI');patchSynctex('%B.synctex.gz')\"";
+
 
=== added file 'example_rcfiles/xelatex_latexmkrc'
--- example_rcfiles/xelatex_latexmkrc	1970-01-01 00:00:00 +0000
+++ example_rcfiles/xelatex_latexmkrc	2012-12-28 00:31:23 +0000
@@ -0,0 +1,20 @@
+# This shows how to use xelatex (http://en.wikipedia.org/wiki/XeTeX)
+# with latexmk.  Xelatex uses Unicode and "supporting modern font
+# technologies such as OpenType or Apple Advanced Typography.
+#
+#   WARNING: latexmk.pl is changing, and plans to have internal
+#     support for xelatex.
+#
+# Since xelatex only produces pdf files, it is a replacement for
+# pdflatex.  To make it your default typesetting engine within latexmk
+# you will not only need to set the $pdflatex variable to require the
+# use of xelatex, but also to turn on production of pdf files and to
+# turn off the production of dvi and ps files, as in the following
+# code: 
+
+
+$pdflatex = 'xelatex %O %S';
+$pdf_mode = 1;
+$postscript_mode = $dvi_mode = 0;
+
+
 
=== added file 'extra-scripts/htlatexonly'
--- extra-scripts/htlatexonly	1970-01-01 00:00:00 +0000
+++ extra-scripts/htlatexonly	2012-12-28 00:31:23 +0000
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+# Replacement for latex executable when latexmk is used for htlatex
+# See TeX4ht-latexmkrc in the example-rcfiles directory of the latexmk
+# distribution for how to use this.
+#
+# This is a shell script suitable for UNIX-like operating systems (including
+# OS-X and linux, and presumably Cygwin under MS-Windows).
+
+latex --recorder $5 '\makeatletter\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\def\Link#1.a.b.c.{\g@addto@macro\@documentclasshook{\RequirePackage[#1,html]{tex4ht}}\let\HCode\documentstyle\def\documentstyle{\let\documentstyle\HCode\expandafter\def\csname tex4ht\endcsname{#1,html}\def\HCode####1{\documentstyle[tex4ht,}\@ifnextchar[{\HCode}{\documentstyle[tex4ht]}}}\makeatother\HCode '$2'.a.b.c.\input ' $1
 
=== added file 'extra-scripts/myhtlatex2'
--- extra-scripts/myhtlatex2	1970-01-01 00:00:00 +0000
+++ extra-scripts/myhtlatex2	2012-12-28 00:31:23 +0000
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+# This is a replacement for htlatex from the TeX4ht package. It allows
+# latexmk to be used to do the latex part of the processing.  
+# See TeX4ht-latexmkrc in the example-rcfiles directory of the latexmk
+# distribution for how to use this.
+#
+# This is a shell script suitable for UNIX-like operating systems (including
+# OS-X and linux, and presumably Cygwin under MS-Windows).
+
+if [[ $# -lt 1  ||  $1 == "--help"  ||  $1 == "-help"  ||  $1 == "-h" ]]; then
+   echo "Convert tex file to html.  Simplest usage"
+   echo "    myhtlatex2 file"
+   exit 1
+fi
+
+latexmk $1
+tex4ht -f/$1  -i~/tex4ht.dir/texmf/tex4ht/ht-fonts/$3
+t4ht -f/$1 $4 ## -d~/WWW/temp/ -m644 
 
=== modified file 'latexmk.1'
--- latexmk.1	2011-06-11 22:09:09 +0000
+++ latexmk.1	2012-12-28 00:31:23 +0000
@@ -1,4 +1,4 @@
-.TH LATEXMK 1L "7 May 2011" ""
+.TH LATEXMK 1L "11 November 2012" ""
 .SH NAME
 latexmk \- generate LaTeX document
 .SH SYNOPSIS
@@ -24,9 +24,9 @@
 .PP
 \fILatexmk\fR determines which are the source files by examining the
 log file.  (Optionally, it also examines the list of input and output
-files generated by the \fI-recorder\fR option of modern versions of
+files generated by the \fB-recorder\fR option of modern versions of
 \fIlatex\fR and \fIpdflatex\fR.  See the documentation for the
-\fI-recorder\fR option of \fIlatexmk\fR below.)
+\fB-recorder\fR option of \fIlatexmk\fR below.)
 When \fIlatexmk\fR is run, it examines properties of the
 source files, and if any have been changed since the last document
 generation, \fIlatexmk\fR will run the various LaTeX processing
@@ -63,8 +63,16 @@
 .PP
 \fILatexmk\fR has the ability to print a banner in gray diagonally
 across each page when making the postscript file.  It can also, if
-needed, call an external program to do other postprocessing on the
-generated files.
+needed, call an external program to do other postprocessing on
+generated dvi and postscript files.  (See the options \fB-dF\fR and
+\fB-pF\fR, and the documentation for the \fI$dvi_filter\fR and
+\fI$ps_filter\fR configuration variables.)  These capabilities are
+leftover from older versions of \fIlatexmk\fR.  More flexibility can
+be obtained in current versions, since the command strings for running
+latex, pdflatex, etc can now be configured to run multiple commands.
+This also extends the possibility of postprocessing generated files to
+pdf files.
+files.
 .PP
 \fILatexmk\fR is highly configurable, both from the command line and
 in configuration files, so that it can accommodate a wide variety of
@@ -89,8 +97,28 @@
 information.
 
 .SH LATEXMK OPTIONS AND ARGUMENTS ON COMMAND LINE
-(All options can be introduced by single or double "-" characters,
-e.g., "latexmk -help" or "latexmk --help".)
+In general the command line to invoke \fIlatexmk\fR has the form
+
+	latexmk [options] [file]
+
+All options can be introduced by single or double "-" characters,
+e.g., "latexmk -help" or "latexmk --help".
+
+\fBNote\fR: In addition to the options in the list below,
+\fIlatexmk\fR recognizes almost all the options recognized by the
+\fIlatex\fR and \fIpdflatex\fR programs in one of both of their
+current TeXLive and MiKTeX implementations.  Some of the options for
+these programs also trigger special action or behavior by
+\fIlatexmk\fR, in which case they are in this list.  Otherwise, they
+are just passed through to a called \fIlatex\fR or \fIpdflatex\fR
+program. Run \fIlatexmk\fR with the \fB-showextraoptions\fR to get a
+list of the options that \fIlatexmk\fR accepts and that are simply
+passed through to \fIlatex\fR or \fIpdflatex\fR.  See also the
+explanation of the \fB-showextraoptions\fR option for more
+information. 
+
+\fBDefinitions of options and arguments\fR
+
 .TP
 .B file
 One or more files can be specified.  If no files are specified,
@@ -107,6 +135,23 @@
 
 then \fIlatexmk\fR will operate on the file "foo.tex".  
 .TP
+
+.B -auxdir=FOO or -aux-directory=FOO
+
+Sets the directory for auxiliary output files of (pdf)latex 
+(.aux, .log etc).  This
+achieves its effect by the \fB-aux-directory\fR option of (pdf)latex,
+which currently is only implemented on the MiKTeX version of
+(pdf)latex.
+
+See also the \fB-outdir\fR/\fB-output-directory\fR options, and the
+\fI$aux_dir\fR, \fI$out_dir\fR, and \fI$search_path_separator\fR
+configuration variables of \fIlatexmk\fR.  In particular, see the
+documentation of \fI$out_dir\fR for some complications on what
+directory names are suitable.
+
+.TP
+
 .B -bibtex 
 When the source file uses bbl files for bibliography, run bibtex or
 biber as needed to regenerate the bbl files.  
@@ -172,8 +217,8 @@
 .B -c
 Clean up (remove) all regeneratable files generated by \fIlatex\fR and
 \fIbibtex\fR or \fIbiber\fR except dvi, postscript and pdf.  These files are a
-combination of log files, aux files, latexmk's database file of source
-file information, 
+combination of log files, aux files, \fIlatexmk\fR's database file of
+source file information, 
 and those with extensions
 specified in the \fI@generated_exts\fR configuration variable.  In addition,
 files with extensions by the \fI$clean_ext\fR configuration variable are
@@ -233,30 +278,32 @@
 \fIlatexmk\fR can determine them.
 
 By default the list of dependent files is sent to stdout (i.e.,
-normally to the screen unless you've redirected latexmk's output).
-But you can set the filename where the list is sent by the
-\fI-deps-out=\fR option.
+normally to the screen unless you've redirected \fIlatexmk\fR's
+output). But you can set the filename where the list is sent by the
+\fB-deps-out=\fR option.
 
 See the section "USING \fIlatexmk\fR WITH \fImake\fR" for
 an example of how to use a dependency list with \fImake\fR.  
 
 Users familiar with GNU \fIautomake\fR and \fIgcc\fR will find that
-the \fI-deps\fR option is very similar in its purpose and results to
-the \fI-M\fR option to \fIgcc\fR.
+the \fB-deps\fR option is very similar in its purpose and results to
+the \fB-M\fR option to \fIgcc\fR.  (In fact, \fIlatexmk\fR also has
+options \fB-M\fR, \fB-MF\fR, and \fB-MP\fR options that behave like
+those of \fIgcc\fR.)
 .TP
 .B  -dependents
-Equivalent to \fI-deps\fR.
+Equivalent to \fB-deps\fR.
 .TP
 .B   -deps-  
 Do not show a list of dependent files after processing.  (This is the
 default.) 
 .TP
 .B  -dependents-
-Equivalent to \fI-deps-\fR.
+Equivalent to \fB-deps-\fR.
 .TP
 .B   -deps-out=FILENAME  
 Set the filename to which the list of dependent files is written.  If
-the FILENAME argument is omitted or set to '-', then the output is
+the FILENAME argument is omitted or set to "-", then the output is
 sent to stdout. 
 
 Use of this option also turns on the output of the list of dependent
@@ -270,7 +317,7 @@
 
 Example usage: To use dviselect to select only the even pages of the dvi file:
 
-	latexmk -dF 'dviselect even' foo.tex
+	latexmk -dF "dviselect even" foo.tex
 .TP
 .B -diagnostics
 Print detailed diagnostics during a run.  This may help for debugging
@@ -356,6 +403,16 @@
 .B -h, -help
 Print help information.
 .TP
+.B -jobname=STRING
+Set the basename of output files(s) to STRING, instead of the default,
+which is the basename of the specified TeX file.
+
+This is like the same option for current implementations of the
+\fIlatex\fR and \fIpdflatex\fR, and the passing of this option to
+these programs is part of \fIlatexmk\fR's implementation of
+\fB-jobname\fR.
+
+.TP
 .B -l
 Run in landscape mode, using the landscape mode for the previewers and
 the dvi to postscript converters.  This option is not normally needed
@@ -365,6 +422,40 @@
 .B -l-
 Turn off \fB-l\fR.
 .TP
+.B -latex="COMMAND"
+This sets the string specifying the command to run latex, and is
+typically used to add desired options.  Since the string normally
+contains spaces, it should be quoted, e.g.,
+
+     latex -latex="latex --shell-escape %O %S"  foo.tex
+
+The specification of the contents of the string are the same as for
+the \fI$latex\fR configuration variable.  Depending on your
+operating system and the command-line shell you are using, you may
+need to change the single quotes to double quotes (or something
+else). 
+
+To set the command for running pdflatex (rather than the command for
+latex) see the \fB-pdflatex\fR option.
+
+Note that the effect of this option can also be achieved by using
+the \fB-e\fR option with a suitable line of Perl code to set the
+\fI$latex\fR variable.  See the explanation of the \fB-e\fR option.
+.TP
+.B -M
+Show list of dependent files after processing.  This is equivalent to
+the \fB-deps\fR option.
+.TP
+.B -MF file
+If a list of dependents is made, the \fB-MF\fR specifies the file to
+write it to. 
+.TP
+.B -MP
+If a list of dependents is made, includes phony target for each source
+file.  If you use the dependents list in a Makefile, the dummy rules
+work around errors make gives if you remove header files without
+updating the Makefile to match.
+.TP
 .B -new-viewer
 When in continuous-preview mode, always start a new viewer to view the
 generated file.  By default, \fIlatexmk\fR will, in continuous-preview
@@ -389,6 +480,31 @@
 \fIbibtex\fR or \fIbiber\fR, which would result in overwriting of the
 bbl files. 
 .TP
+.B -norc
+Turn off the automatic reading of initialization (rc) files.
+
+N.B. Normally the initialization files are read and obeyed, and then
+command line options are obeyed in the order they are encountered.
+Then \fB-norc\fR is an exception to this rule: it is acted on first,
+no matter where is occurs on the command line.
+.TP
+
+.B -outdir=FOO or -output-directory=FOO
+
+Sets the directory for the output files of (pdf)latex.  This achieves
+its effect by the \fB-output-directory\fR option of (pdf)latex, which
+currently (Dec. 2011) is implemented on the common versions of
+(pdf)latex, i.e., MiKTeX and TeXLive.  It may not be present in other
+versions. 
+
+See also the \fB-auxdir\fR/\fB-aux-directory\fR options, and the
+\fI$aux_dir\fR, \fI$out_dir\fR, and \fI$search_path_separator\fR
+configuration variables of \fIlatexmk\fR.  In particular, see the
+documentation of \fI$out_dir\fR for some complications on what
+directory names are suitable.
+
+.TP
+
 .B -p
 Print out the document.  By default it is
 the generated postscript file that is printed.  But you can use the
@@ -409,7 +525,9 @@
 so it turns them off. 
 .TP
 .B -pdf
-Generate pdf version of document using pdflatex.
+Generate pdf version of document using pdflatex.  (See the
+\fB-xelatex\fR if you wish to use \fIxelatex\fR to make your pdf
+file(s).) 
 .TP
 .B -pdfdvi
 Generate pdf version of document from the dvi file, by default using dvipdf.
@@ -424,6 +542,26 @@
 It may get overridden if some other option requires the generation of
 a pdf file.)
 .TP
+.B -pdflatex="COMMAND"
+This sets the string specifying the command to run pdflatex, and is
+typically used to add desired options.  Since the string normally
+contains spaces, it should be quoted, e.g.,
+
+     latex -pdf -pdflatex="pdflatex --shell-escape %O %S"  foo.tex
+
+The specification of the contents of the string are the same as for
+the \fI$pdflatex\fR configuration variable.  Depending on your
+operating system and the command-line shell you are using, you may
+need to change the single quotes to double quotes (or something
+else). 
+
+To set the command for running latex (rather than the command for
+pdflatex) see the \fB-latex\fR option.
+
+Note that the effect of this option can also be achieved by using
+the \fB-e\fR option with a suitable line of Perl code to set the
+\fI$pdflatex\fR variable. See the explanation of the \fB-e\fR option.
+.TP
 .B -print=dvi, -print=ps, -print=pdf
 Define which kind of file is printed.  This option also ensures that
 the requisite file is made, and turns on printing.  The default is to
@@ -491,11 +629,11 @@
 bug in gv that causes an error when the newly updated pdf file is
 read.)  Many other previewers will need a manual update.
 
-Important note: the acroread program on MS-Windows locks the pdf file,
+\fBImportant note\fR: the acroread program on MS-Windows locks the pdf file,
 and prevents new versions being written, so it is a bad idea to use
-acroread to view pdf files in preview-continuous mode.  It is better
-to use a dvi or ps viewer, as set by one of the \fB-view=dvi\fR and
-\fB-view=ps\fR options.
+acroread to view pdf files in preview-continuous mode.  
+It is better to use a different viewer: SumatraPDF and gsview are
+good possibilities. 
 
 There are some other methods for arranging an update, notably useful
 for many versions of xdvi and xpdf.  These are best set in
@@ -558,6 +696,39 @@
 Do not show a list of \fIlatexmk\fR's rules and dependencies after
 processing.  (This is the default.)
 .TP
+.B -showextraoptions
+Show the list of extra \fIlatex\fR and \fIpdflatex\fR options that
+\fIlatexmk\fR recognizes.  These are options for the \fIlatex\fR and
+\fIpdflatex\fR that \fIlatexmk\fR recognizes, but simply passes
+through to these programs when they are run.  These options are
+(currently) a combination of those allowed by the TeXLive and MiKTeX
+implementations.  (If a particular option is given to \fIlatexmk\fR
+but is not handled by the particular implementation of \fIlatex\fR or
+\fIpdflatex\fR that is being used, that program will probably give an
+error message.)  These options are very numerous, but are not listed
+in this documentation because they have no effect on \fIlatexmk\fR's
+actions.
+
+There are a few options (\fB-includedirectory=dir\fR,
+\fB-initialize\fR, \fB-ini\fR) that are not recognized, either because
+they don't fit with \fIlatexmk\fR's intended operations, or because
+they need special processing by \fIlatexmk\fR that isn't implemented
+(at least, not yet).
+
+There are also options that are accepted by \fIlatex\fR etc, but
+instead trigger actions by \fIlatexmk\fR: \fB-help\fR,
+\fB-version\fR. 
+
+Finally, there are certain options for \fIlatex\fR and \fIpdflatex\fR
+(e.g., \fB-recorder\fR) that trigger special actions or behavior by
+\fIlatexmk\fR itself as well as being passed in some form to the
+called \fIlatex\fR and \fIpdflatex\fR program, or that affect other
+programs as well.  These options do have entries in this
+documentation.  These options are:
+\fB-jobname=STRING\fR, \fB-aux-directory=dir\fR,
+\fB-output-directory=DIR\fR, \fB-quiet\fR, and \fB-recorder\fR.
+
+.TP
 .B -silent
 Run commands silently, i.e., with options that reduce the amount of
 diagnostics generated.  For example, with the default settings, the
@@ -569,9 +740,9 @@
 To change the options used to make the commands run silently, you need
 to configure \fIlatexmk\fR with changed values of its configuration
 variables, the relevant ones being \fI$bibtex_silent_switch\fR,
-\fI$biber_silent_switch\fR,
-\fI$dvips_silent_switch\fR, \fI$latex_silent_switch\fR, and
-\fI$pdflatex_silent_switch\fR.
+\fI$biber_silent_switch\fR, \fI$dvipdf_silent_switch\fR, 
+\fI$dvips_silent_switch\fR, \fI$latex_silent_switch\fR, 
+\fI$makeindex_silent_switch\fR, and \fI$pdflatex_silent_switch\fR.
 .TP
 .B -use-make
 When after a run of \fIlatex\fR or \fIpdflatex\fR, there are warnings
@@ -604,6 +775,14 @@
 Set the kind of file used when previewing is requested (e.g., by the
 \fB-pv\fR or \fB-pvc\fR switches).  The default is to view the "highest"
 kind of requested file (in the order dvi, ps, pdf).  
+.TP
+.B -xelatex
+Use xelatex.  That is, use xelatex to process the source file(s) to
+pdf (in place of pdflatex).  This option is exactly equivalent to
+specifying the following sequence of options: 
+
+     -pdflatex="xelatex %O %S" -pdf -dvi- -ps
+
 .PP
 The preview-continuous option \fB-pvc\fR can only work with one file.
 So in this case you will normally only specify one filename on
@@ -647,16 +826,19 @@
    "/usr/local/lib/latexmk/LatexMk".
    On a MS-WINDOWS system it looks for "C:\\latexmk\\LatexMk".
    On a cygwin system (i.e., a MS-Windows system in which perl is
-   that of cygwin), \fIlatexmk\fR reads for the first it finds of
+that of cygwin), \fIlatexmk\fR reads for the first it finds of
    "/cygdrive/c/latexmk/LatexMk",
    "/opt/local/share/latexmk/LatexMk",
    "/usr/local/share/latexmk/LatexMk",
    "/usr/local/lib/latexmk/LatexMk".
 .PP
 2) The user's RC file, "$HOME/.latexmkrc", if it exists.  Here $HOME
-is the value of the environment variable HOME.  On UNIX and clones
-(including LINUX), this variable is set by the system; on MS-Windows,
-the user may choose to set it.
+is the user's home directory.  [\fILatexmk\fR determines the user's
+home directory as follows:  It is the value of the environment variable
+HOME, if this variable exists, which normally is the case on UNIX-like
+systems (including LINUX and OS-X).  Otherwise the environment
+variable USERPROFILE is used, if it exists, which normally is the case
+on MS-Windows systems. Otherwise a blank string is used instead of $HOME.]
 .PP
 3) The RC file in the current working directory.  This file can be
 named either "latexmkrc" or ".latexmkrc", and the first of these to be
@@ -679,6 +861,12 @@
 \fB-e\fR option, which allows initialization code to be specified in
 \fIlatexmk\fR's command line.
 
+\fI
+For possible examples of code for in an RC file, see the directory
+example_rcfiles in the distribution of latexmk (e.g., at
+http://ctan.tug.org/tex-archive/support/latexmk/example_rcfiles).
+\fR
+
 .SH HOW TO SET VARIABLES IN INITIALIZATION FILES
 .PP
 The important variables that can be configured are described in the
@@ -759,6 +947,20 @@
 .TP
 .B %T
 The name of the primary tex file.
+.TP
+.B %Y
+Name of directory for auxiliary output files (see the configuration
+variable \fI$aux_dir\fR).  A directory separation character ('/') is
+appended if \fI$aux_dir\fR is non-empty and does not end in a suitable
+character, with suitable characters being those appropriate to UNIX
+and MS-Windows, i.e., ':', '/' and '\\'. 
+.TP
+.B %Z
+Name of directory for output files (see the configuration
+variable \fI$out_dir\fR).  A directory separation character ('/') is
+appended if \fI$out_dir\fR is non-empty and does not end in a suitable
+character, with suitable characters being those appropriate to UNIX
+and MS-Windows, i.e., ':', '/' and '\\'. 
 .PP
 If for some reason you need a literal % character in your string not
 subject to the above rules, use a pair of these characters.  Thus with
@@ -768,7 +970,7 @@
 name of a postscript file to be viewed. 
 .PP
 Appropriate quoting will be applied to the filename substitutions, so
-you mustn't supply them yourself even if you the names of your have
+you mustn't supply them yourself even if the names of your files have
 spaces in them.  (But if your TeX filenames have spaces in them,
 beware that many versions of the TeX program cannot correctly handle
 filenames containing spaces.)  In case latexmk's quoting does not work
@@ -828,6 +1030,9 @@
 should be enclosed in double quotes, as in
 .PP
      $lpr_pdf = '"c:/Program Files/Ghostgum/gsview/gsview32.exe" /p %S';
+     $pdf_previewer = 'start "c:/Program Files/SumatraPDF/SumatraPDF.exe" %O %S';
+     $pdf_previewer = 'start "c:/Program Files/SumatraPDF (x86)/SumatraPDF.exe" %O %S';
+
 .PP
 (Note about the above example: Forward slashes are equivalent to
 backslashes in filenames under MS-Windows, provided that the filename
@@ -836,6 +1041,14 @@
 about the rules for dealing with forward slashes in strings in the
 Perl language.)
 
+\fBCommand names under Cygwin\fR: If latexmk is executed by Cygwin's
+perl, \fI be particularly certain that pathnames in commands have
+\fBforward\fI slashes\fR not the usual backslashes for the separator
+of pathname components.  See the above examples.  Backslashes often
+get misinterpreted by the Unix shell used by Cygwin's Perl to execute
+external commands.  Forward slashes don't suffer from this problem,
+and (when quoted, as above) are equally acceptable to MS-Windows.
+
 \fBUsing MS-Windows file associations\fR: A useful trick under modern
 versions of MS-Windows (e.g., WinXP) is to use just the 
 command 'start' by itself:
@@ -844,7 +1057,11 @@
 .PP
 Under recent versions of MS-Windows, this will cause to be run
 whatever program the system has associated with dvi files.  (The same
-applies for a postscript viewer and a pdf viewer.)  
+applies for a postscript viewer and a pdf viewer.)  But note that this
+trick is not always suitable for the pdf previwer, if your system has
+acroread for the default pdf viewer.  As explained elsewhere, acroread
+under MS-Windows does not work well with \fIlatex\fR and
+\fIlatexmk\fR, because acroread locks the pdf file.
 
 \fBNot using a certain command\fR: If a command is not to be run, the
 command name NONE is used, as in
@@ -864,6 +1081,17 @@
      $latex = 'latex --src-specials %O %S';
 .PP
 
+\fBRunning a subroutine instead of an external command\fR: Use a
+specification starting with "internal", as in 
+.PP
+     $latex = 'internal mylatex %O %S';
+     sub mylatex {
+         my @args = @_;
+         # Possible preprocessing here
+         return system 'latex', @args;
+     }
+.PP
+
 \fBAdvanced tricks\fR: Normally one specifies a single command for the
 commands invoked by \fIlatexmk\fR.  Naturally, if there is some
 complicated additional processing you need to do in your special
@@ -878,10 +1106,20 @@
 
      $pdflatex = 'pdflatex --shell-escape %O %S; pst2pdf_for_latexmk %B';
 
-This definition assumes you are using a UNIX-like system, so that the
+This definition assumes you are using a UNIX-like system (which
+includes Linux and OS-X), so that the
 two commands to be run are separated by the semicolon in the middle of
-the string.  
-
+the string.
+
+If you are using MS-Windows, you would replace the above line by 
+
+   $pdflatex = 'cmd /c pdflatex --shell-escape %O %S'
+               . '&& pst2pdf_for_latexmk %B';
+
+Here, the UNIX command separator ; is replaced by &&.  In addition,
+there is a problem that some versions of \fIPerl\fR on MS-Windows do
+not obey the command separator; this problem is overcome by explicitly
+invoking the MS-Windows command-line processor \fIcmd.exe\fR.
 
 .SH LIST OF CONFIGURATION VARIABLES USABLE IN INITIALIZATION FILES
 .PP
@@ -904,6 +1142,34 @@
 file is created. 
 
 .TP
+.B $auto_rc_use [1]
+Whether to automatically read the standard initialization (rc) files,
+which are the system RC file, the user's RC file, and the RC file in
+the current directory.  The command line option \fB-norc\fR can be
+used to turn this setting off.  Each RC file could also turn this
+setting off, i.e., it could set \fI$auto_rc_use\fR to zero to prevent
+automatic reading of the later RC files.
+
+This variable does not affect the reading of RC files specified on the
+command line by the \fB-r\fR option.
+
+.TP
+.B $aux_dir [""]
+The directory in which auxiliary files (aux, log, etc) are to be
+written by a run of (pdf)latex.  If this variable is not set, but 
+\fI$out_dir\fR is set, then \fI$aux_dir\fR is set to \fI$out_dir\fR,
+which is the directory to which general output files are to be
+written. 
+
+\fBImportant note\fR:  The effect of \fI$aux_dir\fR, if different from
+\fI$out_dir\fR, is achieved by giving (pdf)latex the
+\fB-aux-directory\fR.  Currently (Dec. 2011) this only works on the
+MiKTeX version of (pdf)latex.
+
+See also the documentation of \fI$out_dir\fR for some complications on
+what directory names are suitable.
+
+.TP
 .B $banner [0]
 If nonzero, the banner message is printed across each page when
 converting the dvi file to postscript.  Without modifying the variable
@@ -953,7 +1219,7 @@
 two and the second two examples are equivalent.  Each backward slash
 should be doubled to avoid running afoul of \fIPerl\fR's rules for writing
 strings. 
-.PP
+
 \fIImportant note:\fR This variable is now mostly obsolete in the
 current version of \fIlatexmk\fR, 
 since it has a better method of searching for files using the
@@ -990,7 +1256,7 @@
 .B $cleanup_includes_cusdep_generated [0]
 If nonzero, specifies that cleanup also deletes files that are
 generated by custom dependencies.
-(When doing a clean up, e.g., by use of the \fI-C\fR option, custom
+(When doing a clean up, e.g., by use of the \fB-C\fR option, custom
 dependencies are those listed in the \fI.fdb_latexmk\fR file from a
 previous run.)
 .TP
@@ -1006,7 +1272,7 @@
 files.  (There is also extra cleaning as specified by the
 \fI$clean_ext\fR, \fI$clean_full_ext\fR and \fI@generated_exts\fR
 variables.)
-.PP
+
 This variable is equivalent to specifying one of
 the \fB-c\fR or \fB-C\fR options.  But there should be no need
 to set this variable from an RC file.
@@ -1032,9 +1298,50 @@
 Extra extensions of files for \fIlatexmk\fR to remove when the \fB-C\fR
 option is selected, i.e., extensions of files to remove when the .dvi,
 etc files are to be cleaned-up.
+
+More general patterns are allowed, as for \fI$clean_ext\fR.
+
+.TP
+.B $compiling_cmd [undefined], $failure_cmd [undefined], $success_cmd [undefined]
+
+These variables specify commands that are executed at certain points
+of compilations during preview-continuous mode.  One motivation for
+their existance is to allow convenient visual indications of
+compilation status even when the window receiving the screen output of
+the compilation is hidden.
+
+The commands are executed at the following points:
+$compiling_cmd at the start of compilation, $success_cmd at the end of
+a successful compilation, and $failure_cmd at the end of an
+unsuccessful compilation.  If any of above variables is undefined (the
+default situation) or blank, then the corresponding command is not
+executed.  
+
+An example of a typical setting of these variables is as follows
+
+    $compiling_cmd = "xdotool search --name \\"%D\\" set_window --name \\"%D compiling\\"";
+    $success_cmd   = "xdotool search --name \\"%D\\" set_window --name \\"%D OK\\"";
+    $failure_cmd   = "xdotool search --name \\"%D\\" set_window --name \\"%D FAILURE\\"";
+
+These assume that the program \fIxdotool\fR is installed, that the
+previewer is using an X-Window system for display, and that the title
+of the window contains the name of the displayed file, as it normally
+does.  When the commands are executed, the placeholder string %D is replaced by
+the name of the destination file, which is the previewed file.  The
+above commands result in an appropriate string being appended to the
+filename in the window title: " compiling", " OK", or " FAILURE".  
+
+Other placeholders that can be used are %S, %T, and %R, with %S and %T
+normally being identical. These can be useful for a command changing
+the title of the edit window. The visual indication in a window title
+can useful, since the user does not have to keep shifting attention to
+the (possibly hidden) compilation window to know the status of the
+compilation.
+
 .TP
 .B @cus_dep_list [()]
 Custom dependency list -- see section on "Custom Dependencies".
+
 .TP
 .B @default_files [("*.tex")]
 Default list of files to be processed.  
@@ -1063,6 +1370,13 @@
 \fI@default_files\fR is an array variable, i.e., a sequence of
 filename specifications is possible.
 .TP
+.B $dependents_phony [0]
+If a list of dependencies is output, this variable determines whether
+to include a phony target for each source file.  If you use the
+dependents list in a Makefile, the dummy rules work around errors make
+gives if you remove header files without updating the Makefile to
+match.
+.TP
 .B $dependents_list [0]
 Whether to display a list(s) of dependencies at the end of a run.
 .TP
@@ -1073,7 +1387,7 @@
 .B $dvi_mode [See below for default]
 If nonzero, generate a dvi version of the document.  
 Equivalent to the \fB-dvi\fR option.
-.PP
+
 The variable $dvi_mode defaults to 0, but if no explicit requests are
 made for other types of file (postscript, pdf), then $dvi_mode will be
 set to 1.  In addition, if a request for a file for which a .dvi file
@@ -1083,7 +1397,18 @@
 The command to invoke a dvi-previewer.
 [Default is "start" under MS-WINDOWS; under more recent versions of
 Windows, this will cause to be run whatever command the system has
-associated with .dvi files.] 
+associated with .dvi files.]
+
+\fBImportant note\fR: Normally you will want to have a previewer run
+detached, so that \fIlatexmk\fR doesn't wait for the previewer to
+terminate before continuing its work.  So normally you should prefix
+the command by "start ", which flags to \fIlatexmk\fR that it should
+do the detaching of the previewer itself (by whatever method is
+appropriate to the operating system).  But sometimes letting
+\fIlatexmk\fR do the detaching is not appropriate (for a variety of
+non-trivial reasons), so you should put the "start " bit in
+yourself, whenever it is needed.
+
 .TP
 .B $dvi_previewer_landscape ["start xdvi %O %S"]
 The command to invoke a dvi-previewer in landscape mode.
@@ -1102,6 +1427,14 @@
 should be modified to give dvips the options "-P pdf" to ensure that
 type 1 fonts are used in the pdf file.
 .TP
+.B $dvipdf_silent_switch ["-q"]
+Switch(es) for dvipdf program when silent mode is on.
+
+N.B. The standard dvipdf program runs silently, so adding the silent
+switch has no effect, but is actually innocuous.  But if an
+alternative program is used, e.g., dvipdfmx, then the silent switch
+has an effect.  The default setting is correct for dvipdfm and dvipdfmx.
+.TP
 .B $dvips ["dvips %O -o %D %S"]
 The program to used as a filter to convert a .dvi file to a .ps file.  
 If pdf is going to be generated from pdf, then the value of the
@@ -1150,6 +1483,9 @@
 \fI$dvi_update_method\fR.  The default value is the one appropriate
 for xdvi on a UNIX system.
 .TP
+.B $failure_cmd [undefined]
+See the documentation for $compiling_cmd.
+.TP
 .B $fdb_ext ["fdb_latexmk"]
 The extension of the file which \fIlatexmk\fR generates to contain a
 database of information on source files.  You will not normally need
@@ -1353,6 +1689,9 @@
 .B $makeindex ["makeindex %O -o %D %S"]
 The index processing program.
 .TP
+.B $makeindex_silent_switch ["-q"]
+\fBSwitch(es)\fR for the index processing program when silent mode is on.
+.TP
 .B $max_repeat  [5]
 The maximum number of times \fIlatexmk\fR will run latex/pdflatex
 before deciding that there may be an infinite loop and that it needs
@@ -1362,6 +1701,23 @@
 (Note that the "etc" covers a lot of cases where one run of
 latex/pdflatex generates files to be read in on a later run.)
 .TP
+.B $MSWin_back_slash [1]
+This configuration variable only has an effect when \fIlatexmk\fR is
+running under MS-Windows.  It determines whether, when a command is
+executed under MS-Windows, there should be substituted "\\" for the
+separator character between components of a directory name.
+Internally, \fIlatexmk\fR uses "/" for the directory separator
+character, which is the character used by Unix-like systems.
+
+For many programs under MS-Windows, both "\\" and "/" are acceptable
+as the directory separator character.  But some programs only accept
+"\\".  So for safety \fIlatexmk\fR makes a translation, by default.
+It is conceivable that under certain situations this is undesirable,
+so the configuration can be changed.  (A possible example might be
+when some of the software is implemented using Cygwin, which provides
+an Unix-like environment inside MS-Windows.)
+
+.TP
 .B $new_viewer_always [0]
 This variable applies to \fIlatexmk\fR \fBonly\fR in
 continuous-preview mode.  If \fI$new_viewer_always\fR is 0,
@@ -1370,6 +1726,34 @@
 \fI$new_viewer_always\fR is non-zero, this check will be skipped, and
 \fIlatexmk\fR will behave as if no viewer is running.
 .TP
+
+.B $out_dir [""]
+The directory in which output files are to be written by a run of
+(pdf)latex.  See also the variable \fI$aux_dir\fR.  
+
+The effect of this variable (when non-blank) is achieved by using the
+\fB-output-directory\fR option of (pdf)latex.  This exists in the
+usual current (Dec. 2011) implementations of TeX, i.e., MiKTeX and
+TeXLive. But it may not be present in other versions.
+
+Commonly, the directory specified for output files is a subdirectory
+of the current working directory.  However, if you specify some other
+directory, e.g., "/tmp/foo" or "../output", be aware that this could
+cause problems, e.g., with \fImakeindex\fR or \fIbibtex\fR.  This is
+because modern versions of these programs, by default, will refuse to
+work when they find that they are asked to write to a file in a
+directory that appears not to be the current working directory or one
+of its subdirectories.  This is part of security measures by the whole
+TeX system that try to prevent malicious or errant TeX documents from
+incorrectly messing with a user's files.  If for \fI$out_dir\fR or
+\fI$aux_dir\fR you really do need to specify an absolute pathname
+(e.g., "/tmp/foo") or a path (e.g., "../output") that includes a
+higher-level directory, then you need to disable the security measures
+(and assume any risks).  This can be done by temporarily setting the
+operating system's environment variable openout_any to "a" (as in
+"all"), to override the default "paranoid" setting.
+.TP
+
 .B $pdf_mode [0]
 If zero, do NOT generate a pdf version of the document.
 If equal to 1, generate a pdf version of the document using pdflatex.  
@@ -1381,9 +1765,24 @@
 Equivalent to the \fB-pdf-\fR, \fB-pdf\fR, \fB-pdfdvi\fR, 
 \fB-pdfps\fR options.
 .TP
+
 .B $pdflatex ["pdflatex %O %S"]
 The LaTeX processing program in the version that makes a pdf file instead
 of a dvi file.
+
+An example of the use of this variable is to arrange for \fIxelatex\fR
+to be used instead of \fIpdflatex\fR, when you could set
+
+     $pdflatex = "xelatex %O %S";
+
+Note that \fIxelatex\fR only produces .pdf files (and not .dvi), so to
+use it you will also need to turn on production of .pdf files, and to
+turn off the production of .dvi (and .ps) files, either by command
+line options or by the following settings in an initialization file
+
+    $pdf_mode = 1; $postscript_mode = $dvi_mode = 0;
+
+
 .TP
 .B %pdflatex_input_extensions
 This variable specifies the extensions tried by latexmk when it finds
@@ -1431,17 +1830,36 @@
 .TP
 .B $pdf_previewer ["start acroread %O %S"]
 The command to invoke a pdf-previewer.
-[Default is changed to "start" on MS-WINDOWS; under more recent versions of
+
+On MS-WINDOWS, the default is changed to "cmd /c start """; under more recent versions of
 Windows, this will cause to be run whatever command the system has
-associated with .pdf files.]  
-
-\fBWARNING\fR: Potential problem under MS-Windows:
+associated with .pdf files.  But this may be undesirable if this
+association is to \fIacroread\fR -- see the notes in the explanation
+of the \fB-pvc\fR option.]  
+
+On OS-X the default is changed to "open %S", which results in OS-X
+starting up (and detaching) the viewer associated with the file.  By
+default, for pdf files this association is to OS-X's preview, which is
+quite satisfactory.
+
+\fBWARNING\fR:  Problem under MS-Windows:
 if acroread is used as the pdf previewer, and it is
 actually viewing a pdf file, the pdf file cannot be updated.  Thus
 makes acroread a bad choice of previewer if you use \fIlatexmk\fR's
 previous-continuous mode (option \fB-pvc\fR) under MS-windows.
-This problem does not occur if ghostview, gv or gsview is used to
-view pdf files.
+This problem does not occur if, for example, SumatraPDF or gsview is
+used to view pdf files.
+
+\fBImportant note\fR: Normally you will want to have a previewer run
+detached, so that \fIlatexmk\fR doesn't wait for the previewer to
+terminate before continuing its work.  So normally you should prefix
+the command by "start ", which flags to \fIlatexmk\fR that it should
+do the detaching of the previewer itself (by whatever method is
+appropriate to the operating system).  But sometimes letting
+\fIlatexmk\fR do the detaching is not appropriate (for a variety of
+non-trivial reasons), so you should put the "start " bit in
+yourself, whenever it is needed.
+
 .TP
 .B $pdf_update_command [""]
 When the pdf previewer is set to be updated by running a command, this
@@ -1490,7 +1908,7 @@
 .B $postscript_mode [0]
 If nonzero, generate a postscript version of the document.  
 Equivalent to the \fB-ps\fR option.
-.PP
+
 If some other request is made for which a postscript file is needed,
 then $postscript_mode will be set to 1.
 .TP
@@ -1541,7 +1959,7 @@
 file before other processing.  Equivalent to specifying the \fB-pF\fR
 option.
 .TP
-.B $ps_previewer ["start gv %O %S", but \(dqstart %O %S" under MS-WINDOWS]
+.B $ps_previewer ["start gv %O %S", but "start %O %S" under MS-WINDOWS]
 The command to invoke a ps-previewer.  (The default under MS-WINDOWS
 will cause to be run whatever command the system has associated 
 with .ps files.)
@@ -1554,8 +1972,19 @@
 \fBWARNING\fR: Linux systems may have installed one (or more) versions
 of gv under different names, e.g., ggv, kghostview, etc, but perhaps
 not one called gv.  
+
+\fBImportant note\fR: Normally you will want to have a previewer run
+detached, so that \fIlatexmk\fR doesn't wait for the previewer to
+terminate before continuing its work.  So normally you should prefix
+the command by "start ", which flags to \fIlatexmk\fR that it should
+do the detaching of the previewer itself (by whatever method is
+appropriate to the operating system).  But sometimes letting
+\fIlatexmk\fR do the detaching is not appropriate (for a variety of
+non-trivial reasons), so you should put the "start " bit in
+yourself, whenever it is needed.
+
 .TP
-.B $ps_previewer_landscape ["start gv -swap %O %S", but \(dqstart %O %S" under MS-WINDOWS]
+.B $ps_previewer_landscape ["start gv -swap %O %S", but "start %O %S" under MS-WINDOWS]
 The command to invoke a ps-previewer in landscape mode.
 .TP
 .B $ps_update_command [""]
@@ -1589,7 +2018,7 @@
 specifications (as in \fI$pdflatex\fR) are surrounded by double
 quotes.  If this variable is 1 (or any other value Perl regards as
 true), then quoting is done.  Otherwise quoting is omitted.  
-.PP
+
 The quoting method used by latexmk is tested to work correctly under
 UNIX systems (including Linux and Mac OS-X) and under MS-Windows.  It
 allows the use of filenames containing special characters, notably
@@ -1599,7 +2028,7 @@
 operating system in passing arguments to programs.)
 .TP
 .B $recorder [0]
-Whether to use the \fI-recorder\fR option to \fIlatex\fR and
+Whether to use the \fB-recorder\fR option to \fIlatex\fR and
 \fIpdflatex\fR. Use of this option results in a file of extension
 \fI.fls\fR containing a list of the files that these programs have
 read and written.  \fILatexmk\fR will then use this file to improve
@@ -1618,6 +2047,33 @@
 named for the program, i.e., latex.fls or pdflatex.fls.  In this
 second case, \fIlatexmk\fR copies the latex.fls or pdflatex.fls to a
 file with the basename of the main LaTeX document, e.g., Document.fls.
+
+.TP
+.B $search_path_separator [See below for default]
+The character separating paths in the environment variables TEXINPUTS,
+BIBINPUTS, and BSTINPUTS.  This variable is mainly used by
+\fIlatexmk\fR when the \fB-outdir\fR, \fB-output-directory\fR,
+\fB-auxdir\fR, and/or \fB-aux-directory\fR options are used.  In that
+case \fIlatexmk\fR needs to communicate appropriately modified search
+paths to $\fIbibtex\fR, \fIdvipdf\fR, \fIdvips\fR, and
+\fI(pdf)latex\fR.  
+
+[Comment to technically savvy readers: \fI(pdf)latex\fR doesn't
+actually need the modified search path, because it corrects it
+internally.  But, surprisingly, \fIdvipdf\fR and \fIdvips\fR do,
+because sometimes graphics files get generated in the output or aux
+directories.] 
+
+The default under MSWin and Cygwin is ';' and under UNIX-like
+operating systems (including Linux and OS-X) is ':'.  Normally the
+defaults give correct behavior.  But there can be difficulties if your
+operating system is of one kind, but some of your software is running
+under an emulator for the other kind of operating system; in that case
+you'll need to find out what is needed, and set
+\fI$search_path_separator\fR explicitly.  (The same goes, of course,
+for unusual operating systems that are not in the MSWin, Linux, OS-X,
+Unix collection.)
+
 .TP
 .B $sleep_time [2]
 The time to sleep (in seconds) between checking for source file
@@ -1635,6 +2091,11 @@
 \fI$texfile_search\fR, it is a string of space-separated filenames, and
 then \fIlatexmk\fR replaces \fI@default_files\fR with the filenames in
 \fI$texfile_search\fR to which is added "*.tex".
+
+.TP
+.B $success_cmd [undefined]
+See the documentation for $compiling_cmd.
+
 .TP
 .B $tmpdir [See below for default]
 Directory to store temporary files that \fIlatexmk\fR may generate while
@@ -1732,7 +2193,7 @@
 
     add_cus_dep( 'fig', 'eps', 0, 'fig2eps' );
     sub fig2eps {
-        system("fig2dev -Leps $_[0].fig $_[0].eps"); 
+        system( "fig2dev -Leps \"$_[0].fig\" \"$_[0].eps\"" ); 
     }
 
 The first line adds a custom dependency that converts a file with
@@ -1760,32 +2221,35 @@
 statement, i.e., the invocation of system, which returns the value 0
 on success.
 
-If you use filenames with spaces in them, and if your LaTeX system and
-all other relevant software correctly handle such filenames, then you
-could put single quotes around filenames in the command line that is
-executed:
-
-    add_cus_dep( 'fig', 'eps', 0, 'fig2eps' );
-    sub fig2eps {
-        system("fig2dev -Lps '$_[0].fig' '$_[0].eps'");
-    }
-
-This causes the invocation of the \fIfig2dev\fR program to have quoted
-filenames; it should therefore work with filenames containing spaces.
-\fBHowever, not all software deals correctly with filenames that
-contain spaces.  Moreover, the rules, if any, for quoting filenames
-vary between operating systems, command shells and individual pieces
-of software, so this code may not always work.\fR
-
 If you use pdflatex instead of latex, then you will probably prefer to
 convert your graphics files to pdf format, in which case you would
 replace the above code in an initialization file by
 
     add_cus_dep( 'fig', 'pdf, 0, 'fig2pdf' );
     sub fig2pdf {
-        system("fig2dev -Lpdf $_[0].fig $_[0].pdf"); 
+        system( "fig2dev -Lpdf \"$_[0].fig\" \"$_[0].pdf\"" ); 
     }
 
+\fBNote 1:\fR In the command lines given in the system commands in the
+above examples, double quotes have been inserted around the file names
+(implemented by '\"' in the Perl language).  They immunize the running
+of the program against special characters in filenames.  Very often
+these quotes are not necessary, i.e., they can be omitted.  But it is
+normally safer to keep them in.  Even though the rules for quoting
+vary between operating systems, command shells and individual pieces
+of software, the quotes in the above examples do not cause problems in
+the cases I have tested.
+
+\fBNote 2:\fR One case in which the quotes are important is when the
+files are in a subdirectory and your operating system is Microsoft
+Windows.  Then the separator character for directory components can be
+either a forward slash '/' or Microsoft's more usual backward slash
+'\\'.  Forward slashes are generated by latexmk, to maintain its
+sanity from software like MiKTeX that mixes both directory
+separators; but their correct use normally requires quoted filenames. 
+(See a log file from a run of MiKTeX (at least in v. 2.9) for an
+example of the use of both directory separators.)
+
 If you have some general custom dependencies defined in the system or
 user initialization file, you may find that for a particular project
 they are undesirable.  So you might want to delete the unneeded ones.
@@ -1816,7 +2280,7 @@
 
     add_cus_dep('ndx', 'nnd', 0, 'makendx2nnd');
     sub makendx2nnd {
-        system("makeindex -o $_[0].nnd $_[0].ndx");
+        system( "makeindex -o \"$_[0].nnd\" \"$_[0].ndx"\" );
     }
 
 (You will need to modify this code if you use filenames
@@ -1854,7 +2318,7 @@
 
     push @cus_dep_list, "fig eps 0 fig2eps";
     sub fig2eps {
-        system("fig2dev -Lps $_[0].fig $_[0].eps");
+        system( "fig2dev -Lps \"$_[0].fig\" \"$_[0].eps\"" );
     }
 
 This method still works, and is equivalent to the earlier code using
@@ -1977,11 +2441,11 @@
 make .pdf files from .fig files produced by the \fIxfig\fR program;
 these are commonly used for graphics insertions in LaTeX documents.
 \fILatexmk\fR is arranged to output a dependency file after each run.
-It is given the \fI-recorder\fR option, which improves its detection
+It is given the \fB-recorder\fR option, which improves its detection
 of files generated during a run of \fIpdflatex\fR; such files should
-not be in the dependency list.  The \fI-e\fR options are used to turn
+not be in the dependency list.  The \fB-e\fR options are used to turn
 off all custom dependencies, and to document this.  Instead the
-\fI-use-make\fR is used to delegate the making of missing files to
+\fB-use-make\fR is used to delegate the making of missing files to
 \fImake\fR itself.
 
 Suppose in the LaTeX file there is a command \\includegraphics{graph},
@@ -2015,8 +2479,8 @@
 Acroread under UNIX/LINUX views pdf, but the file needs to be closed
 and reopened to view an updated version.
 Under MS-Windows, acroread locks its input file and so the
-pdf file cannot be updated.  (Remedy: configure \fIlatexmk\fR to use gsview
-instead.) 
+pdf file cannot be updated.  (Remedy: configure \fIlatexmk\fR to use
+\fIsumatrapdf\fR instead.) 
 .SH THANKS TO
 Authors of previous versions.  Many users with their feedback, and
 especially 
@@ -2027,7 +2491,7 @@
 harvested by worms and viruses.)
 .SH AUTHOR
 Current version, by John Collins (username collins at node phys.psu.edu).
-(Version 4.24).
+(Version 4.35).
 
 Released version can be obtained from CTAN:
 <http://www.tug.org/tex-archive/support/latexmk/>, and from the
 
=== modified file 'latexmk.bat'
--- latexmk.bat	2006-06-12 00:43:25 +0000
+++ latexmk.bat	2012-12-28 00:31:23 +0000
@@ -1,5 +1,5 @@
-Rem Execute latexmk.pl, searching for it in the PATH
-Rem Assume perl is in the PATH.  If not, you should replace 'perl' by 
-Rem the full pathname of the perl executable, e.g., 'C:\perl\bin\perl.exe'
-
-perl -S latexmk.pl %1 %2 %3 %4 %5 %6 %7 %8 %9
+Rem Execute latexmk.pl, searching for it in the PATH
+Rem Assume perl is in the PATH.  If not, you should replace 'perl' by 
+Rem the full pathname of the perl executable, e.g., 'C:\perl\bin\perl.exe'
+
+perl -S latexmk.pl %1 %2 %3 %4 %5 %6 %7 %8 %9
 
=== modified file 'latexmk.pdf'
 Binary files latexmk.pdf	2011-06-11 22:09:09 +0000 and latexmk.pdf	2012-12-28 00:31:23 +0000 differ
=== modified file 'latexmk.pl'
--- latexmk.pl	2011-06-11 22:09:09 +0000
+++ latexmk.pl	2012-12-28 00:31:23 +0000
@@ -1,4 +1,8 @@
 #!/usr/bin/env perl
+
+# N.B. !!!!!!!!!!!  See 17 July 2012 comments !!!!!!!!!!!!!!!!!!
+
+
 # On a UNIX-like system, the above enables latexmk to run independently
 #   of the location of the perl executable.  This line relies on the 
 #   existence of the program /usr/bin/env
@@ -9,7 +13,6 @@
 
 # with the path of the perl executable adjusted for your system. 
 
-
 use warnings;
 
 # Delete #??!! when working
@@ -22,6 +25,7 @@
 ## (I have hooks for this).
 
 
+
 #=======================================
 
 #??  Force mode doesn't appear to do force (if error in latex file)
@@ -107,15 +111,15 @@
 
 $my_name = 'latexmk';
 $My_name = 'Latexmk';
-$version_num = '4.24';
-$version_details = "$My_name, John Collins, 7 May 2011";
-
+$version_num = '4.35';
+$version_details = "$My_name, John Collins, 11 Nov. 2012";
 
 use Config;
 use File::Copy;
 use File::Basename;
 use FileHandle;
 use File::Find;
+use List::Util qw( max );
 use Cwd;            # To be able to change cwd
 use Cwd "chdir";    # Ensure $ENV{PWD}  tracks cwd
 use Digest::MD5;
@@ -141,7 +145,7 @@
    warn "Something wrong with the perl configuration: No signals?\n";
 }
 
-## Copyright John Collins 1998-2011
+## Copyright John Collins 1998-2012
 ##           (username collins at node phys.psu.edu)
 ##      (and thanks to David Coppit (username david at node coppit.org) 
 ##           for suggestions) 
@@ -175,37 +179,94 @@
 ##     5.  Parsing of log file instead of source file is used to
 ##         obtain dependencies, by default.
 ##
-##   Modification log from 1 Jan 2011 onwards in detail
+##   Modification log from 9 Dec 2011 onwards in detail
 ##
-##      7 May 2011, John Collins  With biber, use kpsewhich to find source
-##                                   files (e.g., .bib)
-##     24 Mar 2011, John Collins  Correct bug in detection of source files
-##                                   listed in .fls
-##     21 Mar 2011, John Collins  Add 'bcf' to list of generated extensions
-##                                Deal with case that fls files are latex.fls
-##                                   and pdflatex.fls
-##     19--21 Mar 2011, John Collins  -deps and -rules options
-##                                $use_make_for_missing_files
-##                                -recorder option
-##     12 Mar 2011, John Collins  Deal with problem that if maximum number of
-##                                runs of (pdf)latex is exceeded, -pvc mode
-##                                infinitely repeats (pdf)latex
-##     11 Mar 2011, John Collins  Fix problem that changes in generated files
-##                                during run of (pdf)latex may not be detected
-##                                if the run is shorter than the granularity 
-##                                of file times.
-##     28 Feb 2011, John Collins  Corrections of comments and messages
-##     22 Feb 2011, John Collins  Documentation improvement.
-##     16 Feb 2011, John Collins  Correctly parse blg files of biber 0.8
-##                                Version 4.23.
-##      3 Feb 2011, John Collins  Correct handling of errors in rc files
-##     23 Jan 2011, John Collins  Fix detection of makeindex files with
-##                                   MiKTeX v >= 2.8
-##     23 Jan 2011, John Collins  Fix detection of biber use with MiKTeX 
-##                            (which doesn't put openout lines in log file).
-##      9 Jan 2011, John Collins  Correct parsing of blg file for biber 0.7.2
-##      3 Jan 2011, John Collins  Small correction on reading .fdb_file
-##      1 Jan 2011, John Collins  Biber implementation
+##   12 Jan 2012 STILL NEED TO DOCUMENT some items below
+##     11 Nov 2012  John Collins  V. 4.35
+##                                Correct bug that under some combinations of
+##                                   MS-Windows, cygwin and distributions of
+##                                   TeX, line endings in fls file (CRLF v. LF)
+##                                   were misparsed, resulting in source
+##                                   filenames that incorrectly contained CR
+##                                   characters.
+##                                Correct bug that when --gg mode is on, the
+##                                   rule database contained items from the OLD
+##                                   fdb file.  Using --gg mode implies that
+##                                   the rules in the OLD fdb file must be
+##                                   ignored (since they may be wrong).
+##      1 Oct 2012  John Collins  V. 4.34
+##                                Correct problem that if a file is read by
+##                                   latex only after being written, it is
+##                                   not a true source file.
+##     19 Aug 2012  John Collins  V. 4.33c
+##                                Correct infinite loop when maximum passes
+##                                   exceeded.
+##                                Improve error messages
+##     12 Aug 2012  John Collins  V. 4.33b
+##                                Improve text displayed by -showextraoptions
+##      8 Aug 2012  John Collins  V. 4.33a
+##                                Fix problem that with Cygwin,
+##                                   latexmk runs very slowly, because 
+##                                   subroutine good_cwd() runs the
+##                                   program cygpath on every
+##                                   invocation.  Solution: cach cwd.
+##      6 Aug 2012  John Collins  Version number to 4.33
+##      4 Aug 2012  John Collins  Further fixes of filename treatment:
+##                                   normalize_filename routine to remove
+##                                   string for current directory, and
+##                                   convert '\' directory separator to '/'
+##                                   (Note MiKTeX uses BOTH, see e.g., its
+##                                   log file, so MSWin systems are NOT
+##                                   guaranteed to be consistent.  But latexmk
+##                                   needs to treat filenames differing by
+##                                   change of directory separator as equivalent.
+##                                   Warning: SOME MWWin programs, e.g., current
+##                                   cmd.exe (as tested yesterday on PSU computer
+##                                   in library) do not accept '/' as directory
+##                                   separator, so it may be worth allowing conversion
+##                                   to '\' in executed files.)
+##                                Also improve running when $silent is on:
+##                                   don't print warnings about undefined references
+##                                   and citations, but simply display a summary, whose
+##                                   criterion for being shown had to be fixed.
+##      3 Aug 2012  John Collins  Fix finding of files in aux-dir
+##      1 Aug 2012  John Collins  Handle aliasing of cwd in output file
+##                                to avoid unnecessary warnings about
+##                                actual o/p file .ne. expected with MiKTeX
+##                                Clean up subroutine names:
+##                       parse_logB to parse_log
+##                       make_preview_continuousB to make_preview_continuous
+##                       rdb_find_new_filesB to rdb_find_new_files
+##                       rdb_set_dependentsA to rdb_set_dependents
+##                       rdb_makeB to rdb_make
+##                       rdb_makeB1 to rdb_make1
+##                       rdb_one_depA to rdb_one_dep
+##                       rdb_recurseA to rdb_recurse
+##                       rdb_update_filesA to rdb_update_files
+##     28, 29, 30 Jul 2012  John Collins  Try better file-name normalization in reading fls file.
+##     18 Jul 2012  John Collins  Change ver. to 4.32d.
+##                                Merge changes from 29 June 2012:
+##                                Add $dvipdf_silent_switch
+##     17 Jul 2012  John Collins  Try better fix for error/rerun and retest issue.
+##                                Now rdb_primary_run doesn't have so many complications
+##                                rdb_makeB's PASS loop is simpler
+##                                rdb_submakeB is unneeded.
+##                                See the lines starting #??
+##                                See comments nearby
+##                                Compare w/ v. 4.32a
+##                                V. 4.32b
+##     17 Jul 2012  John Collins  Fix problem that after finding error in a run
+##                                  of (pdf)latex, latexmk didn't check for
+##                                  changed files before giving up.
+##                                  To do that, I reverted some changes in
+##                                  rdb_primary_run to pre v. 4.31
+##                                Remove unused code
+##                                v. 4.32a
+##      8 May 2012  John Collins  Possibility to substitute backslashes for
+##                                  forward slashes in file and directory
+##                                  names in executed command line,
+##                                  for MSWin
+##      5 May 2012  John Collins  Comment on ctrl/C handling in WAIT loop
 ##
 ##   1998-2010, John Collins.  Many improvements and fixes.
 ##       See CHANGE-log.txt for full list, and CHANGES for summary
@@ -325,6 +386,7 @@
     '^LaTeX Warning: File `([^\\\']*)\\\' not found',
     '^Package .* [fF]ile `([^\\\']*)\\\' not found',
     'Error: pdflatex \(file ([^\)]*)\): cannot find image file',
+    ': File (.*) not found:\s*$',
 );
 
 ## Hash mapping file extension (w/o period, e.g., 'eps') to a single regexp,
@@ -369,9 +431,152 @@
 #        'pdflatex' => { 'tex' => 1, 'pdf' => 1, 'jpg' => 1, 'png' => 1 }; );
 # Instead we'll exercise the user-friendly access routines:
 add_input_ext( 'latex', 'tex', 'eps' );
-add_input_ext( 'pdflatex', 'tex', 'jpg', 'pdf' );
+add_input_ext( 'pdflatex', 'tex', 'jpg', 'pdf', 'png' );
 #show_input_ext( 'latex' ); show_input_ext( 'pdflatex' );
 
+# Information about options to latex and pdflatex that latexmk will simply
+#   pass through to (pdf)latex
+# Option without arg. maps to itself.
+# Option with arg. maps the option part to the full specification
+#  e.g., -kpathsea-debug => -kpathsea-debug=NUMBER
+%allowed_latex_options = ();
+%allowed_latex_options_with_arg = ();
+foreach ( 
+  #####
+  # TeXLive options
+    "-draftmode              switch on draft mode (generates no output PDF)",
+    "-enc                    enable encTeX extensions such as \\mubyte",
+    "-etex                   enable e-TeX extensions",
+    "-file-line-error        enable file:line:error style messages",
+    "-no-file-line-error     disable file:line:error style messages",
+    "-fmt=FMTNAME            use FMTNAME instead of program name or a %& line",
+    "-halt-on-error          stop processing at the first error",
+    "-interaction=STRING     set interaction mode (STRING=batchmode/nonstopmode/\n".
+    "                           scrollmode/errorstopmode)",
+    "-ipc                    send DVI output to a socket as well as the usual\n".
+    "                           output file",
+    "-ipc-start              as -ipc, and also start the server at the other end",
+    "-kpathsea-debug=NUMBER  set path searching debugging flags according to\n".
+    "                           the bits of NUMBER",
+    "-mktex=FMT              enable mktexFMT generation (FMT=tex/tfm/pk)",
+    "-no-mktex=FMT           disable mktexFMT generation (FMT=tex/tfm/pk)",
+    "-mltex                  enable MLTeX extensions such as \charsubdef",
+    "-output-comment=STRING  use STRING for DVI file comment instead of date\n".
+    "                           (no effect for PDF)",
+    "-output-format=FORMAT   use FORMAT for job output; FORMAT is `dvi\" or `pdf\"",
+    "-parse-first-line       enable parsing of first line of input file",
+    "-no-parse-first-line    disable parsing of first line of input file",
+    "-progname=STRING        set program (and fmt) name to STRING",
+    "-shell-escape           enable \\write18{SHELL COMMAND}",
+    "-no-shell-escape        disable \\write18{SHELL COMMAND}",
+    "-shell-restricted       enable restricted \\write18",
+    "-src-specials           insert source specials into the DVI file",
+    "-src-specials=WHERE     insert source specials in certain places of\n".
+    "                           the DVI file. WHERE is a comma-separated value\n".
+    "                           list: cr display hbox math par parend vbox",
+    "-synctex=NUMBER         generate SyncTeX data for previewers if nonzero",
+    "-translate-file=TCXNAME use the TCX file TCXNAME",
+    "-8bit                   make all characters printable by default",
+
+  #####
+  # MikTeX options not in TeXLive
+    "-alias=app              pretend to be app",
+    "-buf-size=n             maximum number of characters simultaneously present\n".
+    "                           in current lines",
+    "-c-style-errors         C-style error messages",
+    "-disable-installer      disable automatic installation of missing packages",
+    "-disable-pipes          disable input (output) from (to) child processes",
+    "-disable-write18        disable the \\write18{command} construct",
+    "-dont-parse-first-line  disable checking whether the first line of the main\n".
+    "                           input file starts with %&",
+    "-enable-enctex          enable encTeX extensions such as \\mubyte",
+    "-enable-installer       enable automatic installation of missing packages",
+    "-enable-mltex           enable MLTeX extensions such as \charsubdef",
+    "-enable-pipes           enable input (output) from (to) child processes",
+    "-enable-write18         fully enable the \\write18{command} construct",
+    "-error-line=n           set the width of context lines on terminal error\n".
+    "                           messages",
+    "-extra-mem-bot=n        set the extra size (in memory words) for large data\n".
+    "                           structures",
+    "-extra-mem-top=n        set the extra size (in memory words) for chars,\n".
+    "                           tokens, et al",
+    "-font-max=n             set the maximum internal font number",
+    "-font-mem-size=n        set the size, in TeX memory words, of the font memory",
+    "-half-error-line=n      set the width of first lines of contexts in terminal\n".
+    "                           error messages",
+    "-hash-extra=n           set the extra space for the hash table of control\n".
+    "                           sequences",
+    "-job-time=file          set the time-stamp of all output files equal to\n".
+    "                           file'stime-stamp",
+    "-main-memory=n          change the total size (in memory words) of the main\n".
+    "                           memory array",
+    "-max-in-open=n          set the maximum number of input files and error\n".
+    "                           insertions that can be going on simultaneously",
+    "-max-print-line=n       set the width of longest text lines output",
+    "-max-strings=n          set the maximum number of strings",
+    "-nest-size=n            set the maximum number of semantic levels\n".
+    "                           simultaneously active",
+    "-no-c-style-errors      standard error messages",
+    "-param-size=n           set the the maximum number of simultaneous macro\n".
+    "                           parameters",
+    "-pool-size=n            set the maximum number of characters in strings",
+    "-record-package-usages=file record all package usages and write them into\n".
+    "                           file",
+    "-restrict-write18       partially enable the \\write18{command} construct",
+    "-save-size=n            set the the amount of space for saving values\n".
+    "                           outside of current group",
+    "-stack-size=n           set the maximum number of simultaneous input sources",
+    "-string-vacancies=n     set the minimum number of characters that should be\n".
+    "                           available for the user's control sequences and font\n".
+    "                           names",
+    "-tcx=name               process the TCX table name",
+    "-time-statistics        show processing time statistics",
+    "-trace                  enable trace messages",
+    "-trace=tracestreams     enable trace messages. The tracestreams argument is\n".
+    "                           a comma-separated list of trace stream names",
+    "-trie-size=n            set the amount of space for hyphenation patterns",
+    "-undump=name            use name as the name of the format to be used,\n".
+    "                           instead of the name by which the program was\n".
+    "                           called or a %& line.",
+
+  #####
+    # Options passed to (pdf)latex that have special processing by latexmk,
+    #   so they are commented out here.
+    #-jobname=STRING         set the job name to STRING
+    #-aux-directory=dir    Set the directory dir to which auxiliary files are written
+    #-output-directory=DIR   use existing DIR as the directory to write files in
+    #-quiet
+    #-recorder               enable filename recorder
+    #
+    # Options with different processing by latexmk than (pdf)latex
+    #-help
+    #-version
+    #
+    # Options NOT used by latexmk
+    #-includedirectory=dir    prefix dir to the search path
+    #-initialize              become the INI variant of the compiler
+    #-ini                     be pdfinitex, for dumping formats; this is implicitly
+    #                          true if the program name is `pdfinitex'
+) {
+    if ( /^([^\s=]+)=/ ) {
+        $allowed_latex_options_with_arg{$1} = $_;
+    }
+    elsif ( /^([^\s=]+)\s/ ) {
+        $allowed_latex_options{$1} = $_;
+    }
+    else {
+        $allowed_latex_options{$_} = $_;
+    }
+}
+
+# Arrays of options that will be added to latex and pdflatex.
+# These need to be stored until after the command line parsing is finished,
+#  in case the values of $latex and/or $pdflatex change after an option
+#  is added.
+@extra_latex_options = ();
+@extra_pdflatex_options = ();
+
+
 ## Command to invoke biber & bibtex
 $biber  = 'biber %O %B';
 $bibtex  = 'bibtex %O %B';
@@ -394,6 +599,12 @@
 
 ## Command to convert dvi file to pdf file directly:
 $dvipdf  = 'dvipdf %O %S %D';
+# N.B. Standard dvipdf runs dvips and gs with their silent switch, so for
+#      standard dvipdf $dvipdf_silent_switch is unneeded, but innocuous. 
+#      But dvipdfmx can be used instead, and it has a silent switch (-q).
+#      So implementing $dvipdf_silent_switch is useful.
+
+$dvipdf_silent_switch  = '-q';
 
 ## Command to convert dvi file to ps file:
 $dvips  = 'dvips %O -o %D %S';
@@ -428,6 +639,10 @@
 ## Current tex's treat extensions like UNIX teTeX:
 $extension_treatment = 'unix';
 
+## Substitute backslashes in file and directory names for
+##  MSWin command line
+$MSWin_back_slash = 1;
+
 $dvi_update_signal = undef;
 $ps_update_signal = undef;
 $pdf_update_signal = undef;
@@ -442,7 +657,8 @@
 
 $quote_filenames = 1;       # Quote filenames in external commands
 
-
+$del_dir = '';        # Directory into which cleaned up files are to be put.
+                      # If $del_dir is '', just delete the files
 
 #########################################################################
 
@@ -459,7 +675,7 @@
 $MSWin_fudge_break = 1; # Give special treatment to ctrl/C and ctrl/break
                         #    in -pvc mode under MSWin
                         # Under MSWin32 (at least with perl 5.8 and WinXP)
-                        #   when latemk is running another program, and the 
+                        #   when latexmk is running another program, and the 
                         #   user gives ctrl/C or ctrl/break, to stop the 
                         #   daughter program, not only does it reach
                         #   the daughter, but also latexmk/perl, so
@@ -570,7 +786,7 @@
     #     example).
     #     Cygwin executables for tex and latex may only know cygwin
     #     filenames. 
-    # 4.  The BIBINPUTS and TEXINPUTS environment variables may be
+    # 4.  The BIBINPUTS environment variables may be
     #     UNIX-style or MSWin-style depending on whether native NT or
     #     cygwin executables are used.  They are therefore parsed
     #     differently.  Here is the clash:
@@ -763,12 +979,29 @@
     }
     elsif ( $^O eq "darwin" ) {
         # OS-X on Macintosh
-        $lpr_pdf  = 'lpr %O %S';  
+        # open starts command associated with a file.
+        # For pdf, this is set by default to OS-X's preview, which is suitable.
+        #     Manual update is simply by clicking on window etc, which is OK.
+        # For ps, this is set also to preview.  This works, but since it
+        #     converts the file to pdf and views the pdf file, it doesn't
+        #     see updates, and a refresh cannot be done.  This is far from
+        #     optimal.
+        # For a full installation of MacTeX, which is probably the most common
+        #     on OS-X, an association is created between dvi files and TeXShop.
+        #     This also converts the file to pdf, so again while it works, it
+        #     does not deal with changed dvi files, as far as I can see.
+        $pdf_previewer = 'open %S';
+        $pdf_update_method = 1;     # manual
+        $dvi_previewer = $dvi_previewer_landscape = 'NONE';
+        $ps_previewer = $ps_previewer_landscape = 'NONE';
+        # Others
+        $lpr_pdf  = 'lpr %O %S';
         $pscmd = "ps -ww -u $ENV{USER}"; 
     }
 }
 
 ## default parameters
+$auto_rc_use = 1;       # Whether to read rc files automatically
 $max_repeat = 5;        # Maximum times I repeat latex.  Normally
                         # 3 would be sufficient: 1st run generates aux file,
                         # 2nd run picks up aux file, and maybe toc, lof which 
@@ -824,10 +1057,14 @@
                         # command line has same effect as with current
                         # tex, etc.  (If $jobname is non-empty, then
                         # the --jobname=... option is used on tex.)
+$out_dir = '';          # Directory for output files.  
+                        # Cf. --output-directory of current (pdf)latex
+$aux_dir = '';          # Directory for aux files (log, aux, etc).
+                        # Cf. --aux-directory of current (pdf)latex in MiKTeX.
 
 
 ## default flag settings.
-$recorder = 0;          # Whether to use recorder option on latex/pdflatex
+$recorder = 1;          # Whether to use recorder option on latex/pdflatex
 $silent = 0;            # silence latex's messages?
 $landscape_mode = 0;	# default to portrait mode
 
@@ -873,9 +1110,14 @@
 $do_cd = 0;     # Do not do cd to directory of source file.
                 #   Thus behave like latex.
 $dependents_list = 0;   # Whether to display list(s) of dependencies
+$dependents_phony = 0;  # Whether list(s) of dependencies includes phony targets
+                        # (as with 'gcc -MP').
 $deps_file = '-';       # File for dependency list output.  Default stdout.
-$rules_list = 0;   # Whether to display list(s) of dependencies
-@dir_stack = (); # Stack of pushed directories.
+$rules_list = 0;        # Whether to display list(s) of dependencies
+@dir_stack = ();        # Stack of pushed directories, each of form of 
+			# pointer to array  [ cwd, good_cwd ], where
+			# good_cwd differs from cwd by being converted
+			# to native MSWin path when cygwin is used.
 $cleanup_mode = 0;      # No cleanup of nonessential LaTex-related files.
                         # $cleanup_mode = 0: no cleanup
                         # $cleanup_mode = 1: full cleanup 
@@ -925,21 +1167,22 @@
 $bad_reference = 0;
 $bad_citation = 0;
 
+# Cache of expensive-to-compute state variables, e.g., cwd in form
+# fixed to deal with cygwin issues.
+%cache = ();
+&cache_good_cwd;
 
 # Set search paths for includes.
 # Set them early so that they can be overridden
 $BIBINPUTS = $ENV{'BIBINPUTS'};
 if (!$BIBINPUTS) { $BIBINPUTS = '.'; }
-#?? OBSOLETE
-$TEXINPUTS = $ENV{'TEXINPUTS'};
-if (!$TEXINPUTS) { $TEXINPUTS = '.'; }
 
 # Convert search paths to arrays:
 # If any of the paths end in '//' then recursively search the
 # directory.  After these operations, @BIBINPUTS  should
 # have all the directories that need to be searched
 
-@BIBINPUTS = find_dirs1 ($BIBINPUTS);
+@BIBINPUTS = find_dirs1( $BIBINPUTS );
 
 
 ######################################################################
@@ -1060,7 +1303,7 @@
 %primaries = ();    # Hash of rules for primary part of make.  Keys are 
                     # currently 'latex', 'pdflatex' or both.  Value is
                     # currently irrelevant.  Use hash for ease of lookup
-   # Make remove this later, if use makeB
+   # Make remove this later, if use rdb_makeB
 
 # Hashes, whose keys give names of particular kinds of rule.  We use
 # hashes for ease of lookup.
@@ -1077,7 +1320,9 @@
                     # Rule data:
                     #   0: [ cmd_type, ext_cmd, int_cmd, test_kind, 
                     #       source, dest, base,
-		    #       out_of_date, out_of_date_user, time_of_last_run, changed
+		    #       out_of_date, out_of_date_user,
+                    #       time_of_last_run, time_of_last_file_check,
+                    #       changed
                     #       last_result, last_message,
                     #       default_extra_generated
                     #      ]
@@ -1087,7 +1332,8 @@
                     #       with substitutions (%D for destination, %S
 		    #       for source, %B for base of current rule,
 		    #       %R for base of primary tex file, %T for
-		    #       texfile name, and %O for options.
+		    #       texfile name, %O for options,
+                    #       %Y for $aux_dir1, and %Z for $out_dir1
                     #     int_cmd specifies any internal command to be
 		    #       used to implement the application of the
 		    #       rule.  If this is present, it overrides
@@ -1135,6 +1381,8 @@
 		    #              last applied.  (In standard units
 		    #              from perl, to be directly compared
 		    #              with file modification times.)
+                    #     time_of_last_file_check = last time that a check
+                    #              was made for changes in source files.
                     #     changed flags whether special changes have been made
                     #          that require file-existence status to be ignored
                     #     last_result is 
@@ -1143,11 +1391,15 @@
                     #                  1 if last run was successful, but
                     #                    failed to create an output file
                     #                  2 if last run failed
+                    #                  200 if last run gave a warning that is
+                    #                    important enough to be reported with 
+                    #                    the error summary.  The warning
+                    #                    message is stored in last_message.
                     #     last_message is error message for last run
                     #     default_extra_generated is a reference to an array
                     #       of specifications of extra generated files (beyond
                     #       the main dest file.  Standard place holders are used.
-                    #       Example ['%R.log'] for (pdf)latex, and ['%R.blg'] 
+                    #       Example ['%Y%R.log'] for (pdf)latex, and ['%R.blg'] 
                     #          for bibtex.  (There's no need for '%R.aux', here,
                     #          since such generated files are detected dynamically.)
                     #   1: {Hash sourcefile -> [source-file data] }
@@ -1185,9 +1437,6 @@
 %fdb_current = ();  # Fdb-hash for all files used.
 
 
-#==================================================
-## Read rc files:
-
 # User's home directory
 $HOME = '';
 if (exists $ENV{'HOME'} ) {
@@ -1198,6 +1447,19 @@
 }
 
 
+#==================================================
+
+# Options that are to be obeyed before rc files are read:
+
+foreach $_ ( @ARGV )
+{
+    if (/^-{1,2}norc$/ ) {
+        $auto_rc_use = 0;
+    }
+}
+
+#==================================================
+## Read rc files with this subroutine
 
 sub read_first_rc_file_in_list {
     foreach my $rc_file ( @_ ) {
@@ -1210,33 +1472,37 @@
     }
 }
 
-# Read system rc file:
-read_first_rc_file_in_list( @rc_system_files );
-# Read user rc file.
-read_first_rc_file_in_list( "$HOME/.latexmkrc" );
-# Read rc file in current directory.
-read_first_rc_file_in_list( "latexmkrc", ".latexmkrc" );
-
-#==================================================
-
-if ($bibtex_use > 1) {
-    push @generated_exts, 'bbl';
-}
-
-#show_array ("BIBINPUTS", @BIBINPUTS); die;
+# Note that each rc file may unset $auto_rc_use to
+# prevent lower-level rc files from being read.
+# So test on $auto_rc_use in each case.
+if ( $auto_rc_use ) {
+    # System rc file:
+    read_first_rc_file_in_list( @rc_system_files );
+}
+if ( $auto_rc_use ) {
+    # User rc file:
+    read_first_rc_file_in_list( "$HOME/.latexmkrc" );
+}
+if ( $auto_rc_use ) { 
+    # Rc file in current directory:
+    read_first_rc_file_in_list( "latexmkrc", ".latexmkrc" );
+}
 
 ## Process command line args.
 @command_line_file_list = ();
 $bad_options = 0;
 
-#print "Command line arguments:\n"; for ($i = 0; $i <= $#ARGV; $i++ ) {  print "$i: '$ARGV[$i]'\n"; }
-
 while ($_ = $ARGV[0])
 {
-  # Make -- and - equivalent at beginning of option:
+  # Make -- and - equivalent at beginning of option,
+  # but save original for possible use in (pdf)latex command line
+  $original = $_;
   s/^--/-/;
   shift;
-  if (/^-bibtex$/) { $bibtex_use = 2; }
+  if ( /^-aux-directory=(.*)$/ || /^-auxdir=(.*)$/ ) {
+      $aux_dir = $1;
+  }
+  elsif (/^-bibtex$/) { $bibtex_use = 2; }
   elsif (/^-bibtex-$/) { $bibtex_use = 0; }
   elsif (/^-nobibtex$/) { $bibtex_use = 0; }
   elsif (/^-bibtex-cond$/) { $bibtex_use = 1; }
@@ -1247,12 +1513,13 @@
   elsif (/^-cd-$/)   { $do_cd = 0; }
   elsif (/^-commands$/) { &print_commands; exit; }
   elsif (/^-d$/)     { $banner = 1; }
-  elsif (/^-dependents$/ || /^-deps$/ ) { $dependents_list = 1; }
+  elsif (/^-dependents$/ || /^-deps$/ || /^-M$/ ) { $dependents_list = 1; }
   elsif (/^-nodependents$/ || /^-dependents-$/ || /^-deps-$/) { $dependents_list = 0; }
   elsif (/^-deps-out=(.*)$/) {
       $deps_file = $1;
       $dependents_list = 1; 
   }
+  elsif (/^-diagnostics/) { $diagnostics = 1; }
   elsif (/^-dvi$/)   { $dvi_mode = 1; }
   elsif (/^-dvi-$/)  { $dvi_mode = 0; }
   elsif (/^-f$/)     { $force_mode = 1; }
@@ -1263,7 +1530,6 @@
      $go_mode = 2; $cleanup_mode = 1; $cleanup_fdb = 1; $cleanup_only = 0; 
   }
   elsif ( /^-h$/ || /^-help$/ )   { &print_help; exit;}
-  elsif (/^-diagnostics/) { $diagnostics = 1; }
   elsif (/^-jobname=(.*)$/) {
       $jobname = $1;
   }
@@ -1272,24 +1538,44 @@
   elsif (/^-latex=(.*)$/) {
       $latex = $1;
   }
-  elsif (/^-pdflatex=(.*)$/) {
-      $pdflatex = $1;
-  }
+  elsif (/^-latexoption=(.*)$/) {
+      push @extra_latex_options, $1;
+      push @extra_pdflatex_options, $1;
+  }
+# See above for -M
+  elsif (/^-MF$/) {
+     if ( $ARGV[0] eq '' ) {
+	&exit_help( "No file name specified after -MF switch");
+     }
+     $deps_file = $ARGV[0];
+     shift; 
+  }
+  elsif ( /^-MP$/ ) { $dependents_phony = 1; }
   elsif (/^-new-viewer$/) {
-                       $new_viewer_always = 1; 
+      $new_viewer_always = 1; 
   }
   elsif (/^-new-viewer-$/) {
-                       $new_viewer_always = 0; 
+      $new_viewer_always = 0;
+  }
+  elsif (/^-norc$/ ) {
+      $auto_rc_use = 0;
+      # N.B. This has already been obeyed.
+  }
+  elsif ( /^-output-directory=(.*)$/ ||/^-outdir=(.*)$/ ) {
+      $out_dir = $1;
   }
   elsif (/^-p$/)     { $printout_mode = 1; 
                        $preview_continuous_mode = 0; # to avoid conflicts
                        $preview_mode = 0;  
                      }
   elsif (/^-p-$/)    { $printout_mode = 0; }
+  elsif (/^-pdf$/)   { $pdf_mode = 1; }
+  elsif (/^-pdf-$/)  { $pdf_mode = 0; }
   elsif (/^-pdfdvi$/){ $pdf_mode = 3; }
+  elsif (/^-pdflatex=(.*)$/) {
+      $pdflatex = $1;
+  }
   elsif (/^-pdfps$/) { $pdf_mode = 2; }
-  elsif (/^-pdf$/)   { $pdf_mode = 1; }
-  elsif (/^-pdf-$/)  { $pdf_mode = 0; }
   elsif (/^-print=(.*)$/) {
       $value = $1;
       if ( $value =~ /^dvi$|^ps$|^pdf$/ ) {
@@ -1317,21 +1603,44 @@
   elsif (/^-recorder-$/ ){ $recorder = 0; }
   elsif (/^-rules$/ ) { $rules_list = 1; }
   elsif (/^-norules$/ || /^-rules-$/ ) { $rules_list = 0; }
+  elsif (/^-showextraoptions$/) {
+     print "List of extra latex and pdflatex options recognized by $my_name.\n",
+           "These are passed as is to (pdf)latex.  They may not be recognized by\n",
+           "particular versions of (pdf)latex.  This list is a combination of those\n",
+           "for TeXLive and MikTeX.\n",
+           "\n",
+           "Note that in addition to the options in this list, there are several\n",
+           "options known to the (pdf)latex programs that are also recognized by\n",
+           "latexmk and trigger special behavior by latexmk.  Since these options\n",
+           "appear in the main list given by running 'latexmk --help', they do not\n",
+           "appear in the following list\n",
+           "\n";
+     foreach $option ( sort( keys %allowed_latex_options, keys %allowed_latex_options_with_arg ) ) {
+       if (exists $allowed_latex_options{$option} ) { print "   $allowed_latex_options{$option}\n"; }
+       if (exists $allowed_latex_options_with_arg{$option} ) { print "   $allowed_latex_options_with_arg{$option}\n"; }
+     }
+     exit;
+  }
   elsif (/^-silent$/ || /^-quiet$/ ){ $silent = 1; }
   elsif (/^-time$/) { $show_time = 1;}
   elsif (/^-time-$/) { $show_time = 0;}
-  elsif (/^-v$/ || /^-version$/)   { 
-      print "\n$version_details. Version $version_num\n"; 
-      exit; 
-  }
   elsif (/^-use-make$/)  { $use_make_for_missing_files = 1; }
   elsif (/^-use-make-$/)  { $use_make_for_missing_files = 0; }
+  elsif (/^-v$/ || /^-version$/)   { 
+      print "\n$version_details. Version $version_num\n";
+      exit;
+  }
   elsif (/^-verbose$/)  { $silent = 0; }
   elsif (/^-view=default$/) { $view = "default";}
   elsif (/^-view=dvi$/)     { $view = "dvi";}
   elsif (/^-view=none$/)    { $view = "none";}
   elsif (/^-view=ps$/)      { $view = "ps";}
   elsif (/^-view=pdf$/)     { $view = "pdf"; }
+  elsif (/^-xelatex$/)      { 
+      $pdflatex = "xelatex %O %S";
+      $pdf_mode = 1;
+      $dvi_mode = $postscript_mode = 0; 
+  }
   elsif (/^-e$/) {  
      if ( $#ARGV < 0 ) {
         &exit_help( "No code to execute specified after -e switch"); 
@@ -1386,6 +1695,13 @@
      $ps_filter = $ARGV[0];
      shift; 
   }
+  elsif ( ( exists( $allowed_latex_options{$_} ) )
+          || ( /^(-.+)=/ && exists( $allowed_latex_options_with_arg{$1} ) )
+        )
+  {
+      push @extra_latex_options, $original;
+      push @extra_pdflatex_options, $original;
+  }
   elsif (/^-/) {
      warn "$My_name: $_ bad option\n"; 
      $bad_options++;
@@ -1403,6 +1719,28 @@
      "**** Report bugs etc to John Collins <collins at phys.psu.edu>. ****\n"
    unless $silent;
 
+if ( ($out_dir ne '') && ($aux_dir eq '') ){
+    $aux_dir = $out_dir;
+}
+
+foreach ($out_dir, $aux_dir) {
+   # Remove aliases to cwd:
+   $_ = normalize_filename( $_ );
+   if ($_ eq '.' ) { $_ = ''; }
+}
+# Versions terminating in directory/path separator
+$out_dir1 = $out_dir;
+$aux_dir1 = $aux_dir;
+foreach ( $aux_dir1, $out_dir1 ) {
+    if ( ($_ ne '')  && ! m([\\/\:]$) ) {
+       $_ .= '/';
+    }
+}
+
+if ($bibtex_use > 1) {
+    push @generated_exts, 'bbl';
+}
+
 # For backward compatibility, convert $texfile_search to @default_files
 # Since $texfile_search is initialized to "", a nonzero value indicates
 # that an initialization file has set it.
@@ -1410,9 +1748,6 @@
     @default_files = split / /, "*.tex $texfile_search";
 }
 
-#printA "A: Command line file list:\n";
-#for ($i = 0; $i <= $#command_line_file_list; $i++ ) {  print "$i: '$command_line_file_list[$i]'\n"; }
-
 #Glob the filenames command line if the script was not invoked under a 
 #   UNIX-like environment.
 #   Cases: (1) MS/MSwin native    Glob
@@ -1431,8 +1766,6 @@
 }
 else {
     @file_list = @command_line_file_list;
-#print "A2:File list:\n";
-#for ($i = 0; $i <= $#file_list; $i++ ) {  print "$i: '$file_list[$i]'\n"; }
 }
 @file_list = uniq1( @file_list );
 
@@ -1526,8 +1859,11 @@
 &fix_cmds;
 
 # Add common options
-add_option( \$latex, $latex_default_switches );
-add_option( \$pdflatex, $pdflatex_default_switches );
+add_option( $latex_default_switches, \$latex );
+add_option( $pdflatex_default_switches, \$pdflatex );
+
+foreach (@extra_latex_options) { add_option( $_, \$latex ); }
+foreach (@extra_pdflatex_options) { add_option( $_, \$pdflatex ); }
 
 
 # If landscape mode, change dvips processor, and the previewers:
@@ -1539,23 +1875,53 @@
 }
 
 if ( $silent ) { 
-    add_option( \$latex, " $latex_silent_switch" ); 
-    add_option( \$pdflatex, " $pdflatex_silent_switch" ); 
-    add_option( \$biber, " $biber_silent_switch" ); 
-    add_option( \$bibtex, " $bibtex_silent_switch" ); 
-    add_option( \$makeindex, " $makeindex_silent_switch" ); 
-    add_option( \$dvips, " $dvips_silent_switch" ); 
+    add_option( "$latex_silent_switch", \$latex );
+    add_option( "$pdflatex_silent_switch", \$pdflatex );
+    add_option( "$biber_silent_switch", \$biber );
+    add_option( "$bibtex_silent_switch", \$bibtex );
+    add_option( "$makeindex_silent_switch", \$makeindex );
+    add_option( "$dvipdf_silent_switch", \$dvipdf );
+    add_option( "$dvips_silent_switch", \$dvips );
 }
 
 if ( $recorder ) {
-    add_option( \$latex, "-recorder" );
-    add_option( \$pdflatex, "-recorder" );
+    add_option( "-recorder", \$latex, \$pdflatex );
+}
+
+if ( $out_dir ) {
+    add_option( "-output-directory=\"$out_dir\"", \$latex, \$pdflatex );
+    if ( ! -e $out_dir ) {
+        warn "$My_name: making output directory '$out_dir'\n"
+	    if ! $silent;
+        mkdir $out_dir;
+    }
+    elsif ( ! -d $out_dir ) {
+        warn "$My_name: you requested output directory '$out_dir',\n",
+             "     but an ordinary file of the same name exists, which will\n",
+             "     probably give an error later\n";
+    }
+}
+
+if ( $aux_dir && ($aux_dir ne $out_dir) ) {
+    # N.B. If $aux_dir and $out_dir are the same, then the -output-directory
+    # option is sufficient, especially because the -aux-directory exists
+    # only in MiKTeX, not in TeXLive.
+    add_option( "-aux-directory=\"$aux_dir\"", \$latex, \$pdflatex );
+    if ( ! -e $aux_dir ) {
+        warn "$My_name: making auxiliary directory '$aux_dir'\n"
+	    if ! $silent;
+        mkdir $aux_dir;
+    }
+    elsif ( ! -d $aux_dir ) {
+        warn "$My_name: you requested aux directory '$aux_dir',\n",
+             "     but an ordinary file of the same name exists, which will\n",
+             "     probably give an error later\n";
+    }
 }
 
 if ( $jobname ne '' ) { 
     $jobstring = "--jobname=$jobname";
-    add_option( \$latex, " $jobstring" ); 
-    add_option( \$pdflatex, " $jobstring" ); 
+    add_option( "$jobstring", \$latex, \$pdflatex );
 }
 
 # Which kind of file do we preview?
@@ -1606,7 +1972,7 @@
 
 if ( $pdf_mode == 2 ) {
     # We generate pdf from ps.  Make sure we have the correct kind of ps.
-    add_option( \$dvips, " $dvips_pdf_switch" );
+    add_option( "$dvips_pdf_switch", \$dvips );
 }
 
 # Note sleep has granularity of 1 second.
@@ -1636,6 +2002,22 @@
     $generated_exts_all{$_} = 1;
 }
 
+if ($aux_dir) {
+    # Ensure $aux_dir is in TEXINPUTS search path.
+    # This is used by dvips for files generated by mpost.
+    if ( ! exists $ENV{TEXINPUTS} ) {
+	# Note the trailing ":" which ensures that the last item
+	# in the list of paths is the empty path, which actually
+	# means the default path, i.e., the following means that
+	# the TEXINPUTS search path is $aux_dir and the standard
+	# value.
+	$ENV{TEXINPUTS} = $aux_dir.$search_path_separator;
+    }
+    elsif ( $ENV{TEXINPUTS} !~ /$aux_dir$search_path_separator/ ) {
+	$ENV{TEXINPUTS} = $aux_dir.$search_path_separator.$ENV{TEXINPUTS};
+    }
+}
+
 $quell_uptodate_msgs = $silent; 
    # Whether to quell informational messages when files are uptodate
    # Will turn off in -pvc mode
@@ -1690,26 +2072,30 @@
         $root_filename = $jobname;
     }
 
+    $aux_main = "$aux_dir1$root_filename.aux";
+    $log_name = "$aux_dir1$root_filename.log";
+    $fdb_name = "$aux_dir1$root_filename.$fdb_ext";
+
     # Initialize basic dependency information:
 
     # For use under error conditions:
-    @default_includes = ($texfile_name, "$root_filename.aux");  
+    @default_includes = ($texfile_name, $aux_main);
 
-    $fdb_file = "$root_filename.$fdb_ext";
-    
-    # Initialize file and rule databases.
+    # Initialize rule database.  
+    # ?? Should I also initialize file database?
     %rule_list = ();
     &rdb_make_rule_list;
     &rdb_set_rules(\%rule_list);
 
     if ( $cleanup_mode > 0 ) {
+# ?? MAY NEED TO FIX THE FOLLOWING IF $aux_dir or $out_dir IS SET.
         my %other_generated = ();
         my @index_bibtex_generated = ();
         my @aux_files = ();
         $have_fdb = 0;
-        if ( -e $fdb_file ) {
-            print "$My_name: Examining fdb file '$fdb_file' for rules ...\n";
-            $have_fdb = ( 0 == rdb_read( $fdb_file ) );
+        if ( -e $fdb_name ) {
+            print "$My_name: Examining fdb file '$fdb_name' for rules ...\n";
+            $have_fdb = ( 0 == rdb_read( $fdb_name ) );
         }
         if ( $have_fdb ) {
             rdb_for_all(
@@ -1733,10 +2119,10 @@
             );
         }
         else {
-            # No fdb file, so do inferior job by parse_logB
-            print "$My_name: Examining log file '$root_filename.log' for generated files...\n";
+            # No fdb file, so do inferior job by parse_log
+            print "$My_name: Examining log file '$log_name' for generated files...\n";
 
-            # Variables set by parse_logB. Can I remove them
+            # Variables set by parse_log. Can I remove them
             local %generated_log = ();
 	    local %dependents = ();    # Maps files to status.  Not used here.
 	    local @bbl_files = ();     # Not used here.
@@ -1745,7 +2131,7 @@
 			 # Maps output file created and read by (pdf)latex
 			 #    to source file of conversion.
 	    local $primary_out = '';   # Actual output file (dvi or pdf). Not used here.
-            &parse_logB;
+            &parse_log;
             %other_generated = %generated_log;
 	}
 
@@ -1776,31 +2162,36 @@
                        ." (only deleted if \$cleanup_includes_generated is set): ",
                         keys %other_generated );
 	}
-        #    files used in previous versions of latexmk
-        &cleanup1( $fdb_ext, 'blg', 'ilg', 'log', 'aux.bak', 'idx.bak', 
+        &cleanup1( $aux_dir1, $fdb_ext, 'blg', 'ilg', 'log', 'aux.bak', 'idx.bak',
                    split(' ',$clean_ext), 
                    keys %generated_exts_all 
                  );
-        unlink( 'texput.log', "texput.aux", 
+        unlink_or_move( 'texput.log', "texput.aux", 
                 keys %index_bibtex_generated, 
                 keys %aux_files );
         if ($cleanup_includes_generated) {
-	    unlink( keys %other_generated );
+	    unlink_or_move( keys %other_generated );
 	}
         if ( $cleanup_includes_cusdep_generated) {
 	    &cleanup_cusdep_generated;
 	}
         if ( $cleanup_mode == 1 ) { 
-            &cleanup1( 'dvi', 'dviF', 'ps', 'psF', 'pdf',
+            &cleanup1( $out_dir1, 'dvi', 'dviF', 'ps', 'psF', 'pdf',
                        split(' ', $clean_full_ext)
                      );
         }
     }
-    if ($cleanup_fdb) { unlink $fdb_file; }
+    if ($cleanup_fdb) {
+       unlink_or_move( $fdb_name );
+       # If the fdb file exists, it will have been read, and therefore changed
+       #   rule database.  But deleting the fdb file implies we also want
+       #   a virgin rule database, so we must reset it:
+       rdb_set_rules( \%rule_list );
+    }
     if ($cleanup_only) { next FILE; }
 
 
-#??? The following are not needed if use makeB.  
+#??? The following are not needed if use rdb_make.  
 #    ?? They may be set too early?
 # Arrays and hashes for picking out accessible rules.
 # Distinguish rules for making files and others
@@ -1826,7 +2217,7 @@
     }
 
     $have_fdb = 0;
-    if ( (! -e $fdb_file) && (! -e "$root_filename.aux") ) {
+    if ( (! -e $fdb_name) && (! -e $aux_main ) ) {
         # No aux and no fdb file => set up trivial aux file 
         #    and corresponding fdb_file.  Arrange them to provoke one run 
         #    as minimum, but no more if actual aux file is trivial.
@@ -1834,8 +2225,8 @@
         &set_trivial_aux_fdb;
     }
 
-    if ( -e $fdb_file ) {
-        $rdb_errors = rdb_read( $fdb_file );
+    if ( -e $fdb_name ) {
+        $rdb_errors = rdb_read( $fdb_name );
         $have_fdb = ($rdb_errors == 0);
     }
     if (!$have_fdb) { 
@@ -1843,10 +2234,10 @@
         # previous run.  So use filetime criterion for make
         # instead of change from previous run, until we have
         # done our own make.
-	rdb_recurseA( [keys %possible_primaries],
+	rdb_recurse( [keys %possible_primaries],
 		      sub{ if ( $$Ptest_kind == 1 ) { $$Ptest_kind = 3;} }
         );
-        if ( -e "$root_filename.log" ) {
+        if ( -e $log_name ) {
 	    rdb_for_some( [keys %possible_primaries], \&rdb_set_latex_deps );
 	}
     }
@@ -1861,7 +2252,7 @@
 
     if ($go_mode) {
         # Force everything to be remade.
-	rdb_recurseA( [keys %requested_filerules], sub{$$Pout_of_date=1;}  );
+	rdb_recurse( [keys %requested_filerules], sub{$$Pout_of_date=1;}  );
     }
 
 
@@ -1873,7 +2264,7 @@
     #************************************************************
 
     if ( $preview_continuous_mode ) { 
-        &make_preview_continuousB; 
+        &make_preview_continuous; 
         # Will probably exit by ctrl/C and never arrive here.
         next FILE;
     }
@@ -1894,7 +2285,7 @@
     #Initialize failure flags now.
     $failure = 0;
     $failure_msg = '';
-    $failure = rdb_makeB( keys %requested_filerules );
+    $failure = rdb_make( keys %requested_filerules );
     if ($failure > 0) { next FILE; }
     rdb_for_some( [keys %one_time], \&rdb_run1 );
 } # end FILE
@@ -1907,7 +2298,8 @@
         if ( $failure_msg ) {
             #Remove trailing space
             $failure_msg =~ s/\s*$//;
-            warn "$My_name: Did not finish processing file:\n   $failure_msg\n";
+            warn "$My_name: Did not finish processing file '$filename':\n",
+                 "   $failure_msg\n";
             $failure = 1;
         }
     }
@@ -1945,7 +2337,8 @@
            @failed_primaries);
     }
     if ( !$force_mode ) {
-      warn "$My_name: Use the -f option to force complete processing.\n";
+      warn "$My_name: Use the -f option to force complete processing,\n",
+           " unless error was exceeding maximum runs of latex/pdflatex.\n";
     }
     exit 12;
 }
@@ -1965,6 +2358,14 @@
         # Source only
         if ( $_ && ! /%/ ) { $_ .= " %O %S"; }
     }
+    foreach ($pdf_previewer, $ps_previewer, $ps_previewer_landscape,
+             $dvi_previewer, $dvi_previewer_landscape,
+    ) {
+        # Run previewers detached
+        if ( $_ && ! /^(nostart|NONE|internal) / ) {
+            $_ = "start $_";
+        }
+    }
     foreach ($biber, $bibtex) {
         # Base only
         if ( $_ && ! /%/ ) { $_ .= " %O %B"; }
@@ -1986,10 +2387,14 @@
 #############################################################
 
 sub add_option {
-    # Call add_option( \$cmd, $opt )
-    # Add option to command
-    if ( ${$_[0]} !~ /%/ ) { &fix_cmds; }
-    ${$_[0]} =~ s/%O/$_[1] %O/;
+    # Call add_option( $opt, \$cmd ... )
+    # Add option to one or more commands
+    my $option = shift;
+    while (@_) {
+        if ( ${$_[0]} !~ /%/ ) { &fix_cmds; }
+        ${$_[0]} =~ s/%O/$option %O/;
+        shift;
+    }
 } #END add_option
 
 #############################################################
@@ -1997,17 +2402,18 @@
 sub rdb_make_rule_list {
 # Substitutions: %S = source, %D = dest, %B = this rule's base
 #                %T = texfile, %R = root = base for latex.
+#                %Y for $aux_dir1, %Z for $out_dir1
 
     # Defaults for dvi, ps, and pdf files
     # Use local, not my, so these variables can be referenced
-    local $dvi_final = "%R.dvi";
-    local $ps_final  = "%R.ps";
-    local $pdf_final = "%R.pdf";
+    local $dvi_final = "%Z%R.dvi";
+    local $ps_final  = "%Z%R.ps";
+    local $pdf_final = "%Z%R.pdf";
     if ( length($dvi_filter) > 0) {
-        $dvi_final = "%R.dviF";
+        $dvi_final = "%Z%R.dviF";
     }
     if ( length($ps_filter) > 0) {
-        $ps_final = "%R.psF";
+        $ps_final = "%Z%R.psF";
     }
 
     my $print_file = '';
@@ -2047,14 +2453,14 @@
 # This is because, especially for dvi file, the contents of the file may contain
 #    a pointer to a file to be included, not the contents of the file! 
     %rule_list = (
-        'latex'    => [ 'primary',  "$latex",     '',            "%T",        "%B.dvi",  "%R", 1, ["%R.log"] ],
-        'pdflatex' => [ 'primary',  "$pdflatex",  '',            "%T",        "%B.pdf",  "%R", 1, ["%R.log"] ],
-        'dvipdf'   => [ 'external', "$dvipdf",    'do_viewfile', $dvi_final,  "%B.pdf",  "%R", 2 ],
-        'dvips'    => [ 'external', "$dvips",     'do_viewfile', $dvi_final,  "%B.ps",   "%R", 2 ],
-        'dvifilter'=> [ 'external', $dvi_filter,  'do_viewfile', "%B.dvi",    "%B.dviF", "%R", 2 ],
-        'ps2pdf'   => [ 'external', "$ps2pdf",    'do_viewfile', $ps_final,   "%B.pdf",  "%R", 2 ],
-        'psfilter' => [ 'external', $ps_filter,   'do_viewfile', "%B.ps",     "%B.psF",  "%R", 2 ],
-        'print'    => [ 'external', "$print_cmd", 'if_source',   $print_file, "",        "",   2 ],
+        'latex'    => [ 'primary',  "$latex",     '',            "%T",        "%Z%B.dvi",  "%R",   1, ["%Y%R.log"] ],
+        'pdflatex' => [ 'primary',  "$pdflatex",  '',            "%T",        "%Z%B.pdf",  "%R",   1, ["%Y%R.log"] ],
+        'dvipdf'   => [ 'external', "$dvipdf",    'do_viewfile', $dvi_final,  "%B.pdf",    "%Z%R", 2 ],
+        'dvips'    => [ 'external', "$dvips",     'do_viewfile', $dvi_final,  "%B.ps",     "%Z%R", 2 ],
+        'dvifilter'=> [ 'external', $dvi_filter,  'do_viewfile', "%B.dvi",    "%B.dviF",   "%Z%R", 2 ],
+        'ps2pdf'   => [ 'external', "$ps2pdf",    'do_viewfile', $ps_final,   "%B.pdf",    "%Z%R", 2 ],
+        'psfilter' => [ 'external', $ps_filter,   'do_viewfile', "%B.ps",     "%B.psF",    "%Z%R", 2 ],
+        'print'    => [ 'external', "$print_cmd", 'if_source',   $print_file, "",          "",     2 ],
         'update_view' => [ 'external', $viewer_update_command, $PA_update,
                                $view_file,  "",        "",   2 ],
         'view'     => [ 'external', "$viewer",    'if_source',   $view_file,  "",        "",   2 ],
@@ -2095,6 +2501,8 @@
 	    # until run time, in case of changes.
 	    foreach ($base, $source, $dest, @$PA_extra_gen ) {
 		s/%R/$root_filename/;
+		s/%Y/$aux_dir1/;
+		s/%Z/$out_dir1/;
 	    }
 	    foreach ($source, $dest ) { 
 		s/%B/$base/;
@@ -2104,7 +2512,7 @@
     #              "    S='$source', D='$dest', B='$base' $needs_making\n";
 	    rdb_create_rule( $rule, $cmd_type, $ext_cmd, $int_cmd, $test_kind, 
 			     $source, $dest, $base,
-			     $needs_making, undef, 1, $PA_extra_gen );
+			     $needs_making, undef, undef, 1, $PA_extra_gen );
 # !! ?? Last line was
 #			     $needs_making, undef, ($test_kind==1) );
 	}
@@ -2156,20 +2564,20 @@
     # 2. Write a corresponding fdb file
     # 3. Provoke a run of (pdf)latex (actually of all primaries). 
 
-    local $aux_file = "$root_filename.aux";
-    open( aux_file, '>', $aux_file )
-        or die "Cannot write file '$aux_file'\n";
+    local *aux_file;
+    open( aux_file, '>', $aux_main )
+        or die "Cannot write file '$aux_main'\n";
     print aux_file "\\relax \n";
     close(aux_file);
 
     foreach my $rule (keys %primaries ) { 
         rdb_ensure_file( $rule, $texfile_name );
-        rdb_ensure_file( $rule, $aux_file );
+        rdb_ensure_file( $rule, $aux_main );
         rdb_one_rule(  $rule,  
                        sub{ $$Pout_of_date = 1; }
                     );
     }
-    &rdb_write( $fdb_file );
+    &rdb_write( $fdb_name );
 } #END set_trivial_aux_fdb
 
 #************************************************************
@@ -2238,12 +2646,21 @@
     my $return = 0;
     my ($base, $path, $ext) = fileparseA( $$Pdest );
     if ( &view_file_via_temporary ) {
-        my $tmpfile = tempfile1( "${root_filename}_tmp", $ext );
-        $return = &rdb_ext_cmd1( '', '', $tmpfile );
-        move( $tmpfile, $$Pdest );
+        if ( $$Pext_cmd =~ /%D/ ) {
+            my $tmpfile = tempfile1( "${root_filename}_tmp", $ext );
+            warn "$My_name: Making '$$Pdest' via temporary '$tmpfile'...\n";
+            $return = &Run_subst( undef, undef, undef, undef, $tmpfile );
+            move( $tmpfile, $$Pdest );
+        }
+        else {
+            warn "$My_name is configured to make '$$Pdest' via a temporary file\n",
+                 "    but the command template '$$Pext_cmd' does not have a slot\n",
+	    "    to set the destination file, so I won't use a temporary file\n";
+            $return = &Run_subst();
+	}
     }
     else {
-        $return = &rdb_ext_cmd;
+        $return = &Run_subst();
     }
     return $return;
 } #END do_viewfile
@@ -2290,7 +2707,7 @@
     }
     elsif ($viewer_update_method == 4) {
         if (defined $$Pext_cmd) {
-            $return = &rdb_ext_cmd;
+            $return = &Run_subst();
 	}
         else {
             warn "$My_name: viewer is supposed to be updated by running a command,\n",
@@ -2306,7 +2723,7 @@
     # Unconditionally apply rule if source file exists.
     # Assumes rule context
     if ( -e $$Psource ) {
-        return &rdb_ext_cmd;
+        return &Run_subst();
     }
     else {
 	return -1;
@@ -2397,7 +2814,7 @@
 
 #************************************************************
 
-sub make_preview_continuousB {
+sub make_preview_continuous {
     local @changed = ();
     local @disappeared = ();
     local @no_dest = ();       # Non-existent destination files
@@ -2405,7 +2822,6 @@
     local @rules_to_apply = ();
 
     local $failure = 0;
-    local $runs = 0;
     local %rules_applied = ();
     local $updated = 0;
 
@@ -2472,7 +2888,10 @@
             #   $MSWin_fudge_break.
             $SIG{BREAK} = $SIG{INT} = 'IGNORE';
         }
-        $failure = rdb_makeB( @targets );
+        if ($compiling_cmd) {
+	    Run_subst( $compiling_cmd );
+        }
+        $failure = rdb_make( @targets );
 
 ##     warn "=========Viewer PID = $$Pviewer_process; updated=$updated\n";
 
@@ -2539,13 +2958,25 @@
             $failure_msg =~ s/\s*$//;  #Remove trailing space
             warn "$My_name: $failure_msg\n",
     "    ==> You will need to change a source file before I do another run <==\n";
+            if ($failure_cmd) {
+	        Run_subst( $failure_cmd );
+            }
 	}
+        else {
+            if ($success_cmd) {
+	        Run_subst( $success_cmd );
+            }
+        }
         rdb_show_rule_errors();
         if ($show_time && ! $first_time) { show_timing(); }
         if ( $first_time || $updated || $failure ) {
             print "\n=== Watching for updated files. Use ctrl/C to stop ...\n";
         }
         $waiting = 1; if ($diagnostics) { warn "WAITING\n"; }
+# During waiting for file changes, handle ctrl/C and ctrl/break here, rather than letting
+#   system handle them by terminating script (and any script that calls it).  This allows,
+#   for example, the clean up code in the following command line to work:
+#          latexmk -pvc foo; cleanup;
         &catch_break;
         $have_break = 0;
   WAIT: while (1) {
@@ -2562,7 +2993,7 @@
            $processing_time1 = processing_time();
         # Does this do this job????
            local $new_files = 0;
-           rdb_for_some( [keys %current_primaries], sub{ $new_files += &rdb_find_new_filesB } );
+           rdb_for_some( [keys %current_primaries], sub{ $new_files += &rdb_find_new_files } );
            if ($new_files > 0) {
 	       warn "$My_name: New file(s) found.\n";
                last WAIT; 
@@ -2576,7 +3007,7 @@
      }
      $waiting = 0; if ($diagnostics) { warn "NOT       WAITING\n"; }
   } #end infinite_loop CHANGE:
-} #END sub make_preview_continuousB
+} #END sub make_preview_continuous
 
 #************************************************************
 
@@ -2585,16 +3016,37 @@
     # NEW VERSION
     # Run rc_file whose name is given in first argument
     #    Exit with code 0 on success
-    #    Exit with code 1 if file could not be read.
+    #    Exit with code 1 if file cannot be read or does not exist.
     #    Stop if there is a syntax error or other problem.
+    # PREVIOUSLY: 
+    #    Exit with code 2 if is a syntax error or other problem.
     my $rc_file = $_[0];
     my $ret_code = 0;
     warn "$My_name: Executing Perl code in file '$rc_file'...\n" 
         if  $diagnostics;
-    if ( ! -r $rc_file ) {
-        return 1;
-    }
-    do( $rc_file );
+    # I could use the do command of perl, but the preceeding -r test
+    # to get good diagnostics gets the wrong result under cygwin
+    # (e.g., on /cygdrive/c/latexmk/LatexMk)
+    my $RCH = new FileHandle;
+    if ( !-e $rc_file ) {
+        warn "$My_name: The rc-file '$rc_file' does not exist\n";
+        return 1;
+    }
+    elsif ( open $RCH, "<$rc_file" ) {
+        { local $/; eval <$RCH>; }
+        close $RCH;
+    }
+    else {
+        warn "$My_name: I cannot read the rc-file '$rc_file'\n";
+        return 1;
+    }
+    # PREVIOUS VERSION
+#    if ( ! -r $rc_file ) {
+#        warn "$My_name: I cannot read the rc-file '$rc_file'\n",
+#  	     "          or at least that's what Perl (for $^O) reports\n";
+#        return 1;
+#    }
+#    do( $rc_file );
     if ( $@ ) {
         # Indent each line of possibly multiline message:
         my $message = prefix( $@, "     " );
@@ -2639,10 +3091,11 @@
 #************************************************************
 
 sub cleanup1 {
-    # Usage: cleanup1( exts_without_period, ... )
+    # Usage: cleanup1( directory, exts_without_period, ... )
+    my $dir = shift;
     foreach (@_) { 
-        (my $name = /%R/ ? $_ : "%R.$_") =~ s/%R/$root_filename/;
-        unlink("$name");
+        (my $name = /%R/ ? $_ : "%R.$_") =~ s/%R/$dir$root_filename/;
+        unlink_or_move("$name");
     }
 } #END cleanup1
 
@@ -2665,7 +3118,7 @@
        return;
     }
     if ( (-e $$Pdest) && (-e $$Psource) ) {
-        unlink $$Pdest;
+        unlink_or_move( $$Pdest );
     }
     elsif ( (-e $$Pdest) && (!-e $$Psource) ) {
         warn "$My_name: For custom dependency '$rule',\n",
@@ -2757,9 +3210,12 @@
   "$My_name $version_num: Automatic LaTeX document generation routine\n\n",
   "Usage: $my_name [latexmk_options] [filename ...]\n\n",
   "  Latexmk_options:\n",
-  "   -bibtex         - use bibtex when needed (default)\n",
-  "   -bibtex-        - never use bibtex\n",
-  "   -bibtex-cond    - use bibtex when needed, but only if the bib files exist\n",
+  "   -aux-directory=dir or -auxdir=dir \n",
+  "                 - set name of directory for auxiliary files (aux, log)\n",
+  "                 - Currently this only works with MiKTeX\n",
+  "   -bibtex       - use bibtex when needed (default)\n",
+  "   -bibtex-      - never use bibtex\n",
+  "   -bibtex-cond  - use bibtex when needed, but only if the bib files exist\n",
   "   -bm <message> - Print message across the page when converting to postscript\n",
   "   -bi <intensity> - Set contrast or intensity of banner\n",
   "   -bs <scale> - Set scale for banner\n",
@@ -2800,10 +3256,17 @@
   "   -l-    - turn off -l\n",
   "   -latex=<program> - set program used for latex.\n",
   "                      (replace '<program>' by the program name)\n",
+  "   -latexoption=<option> - add the given option to the (pdf)latex command\n",
+  "   -M     - Show list of dependent files after processing\n",
+  "   -MF file - Specifies name of file to receives list dependent files\n",
+  "   -MP    - List of dependent files includes phony target for each source file.\n",
   "   -new-viewer    - in -pvc mode, always start a new viewer\n",
   "   -new-viewer-   - in -pvc mode, start a new viewer only if needed\n",
   "   -nobibtex      - never use bibtex\n",
   "   -nodependents  - Do not show list of dependent files after processing\n",
+  "   -norc          - omit automatic reading of system, user and project rc files\n",
+  "   -output-directory=dir or -outdir=dir\n",
+  "                  - set name of directory for output files\n",
   "   -pdf   - generate pdf by pdflatex\n",
   "   -pdfdvi - generate pdf by dvipdf\n",
   "   -pdflatex=<program> - set program used for pdflatex.\n",
@@ -2824,12 +3287,17 @@
   "                on force mode, so errors do not cause $my_name to stop.)\n",
   "            (Side effect: turn off ordinary preview mode.)\n",
   "   -pvc-  - turn off -pvc\n",
+  "   -quiet    - silence progress messages from called programs\n",
   "   -r <file> - Read custom RC file\n",
+  "               (N.B. This file could override options specified earlier\n",
+  "               on the command line.)\n",
   "   -recorder - Use -recorder option for (pdf)latex\n",
   "               (to give list of input and output files)\n",
   "   -recorder- - Do not use -recorder option for (pdf)latex\n",
   "   -rules    - Show list of rules after processing\n",
   "   -rules-   - Do not show list of rules after processing\n",
+  "   -showextraoptions  - Show other allowed options that are simply passed\n",
+  "               as is to latex and pdflatex\n",
   "   -silent   - silence progress messages from called programs\n",
   "   -time     - show CPU time used\n",
   "   -time-    - don't show CPU time used\n",
@@ -2843,14 +3311,18 @@
   "   -view=none    - no viewer is used\n",
   "   -view=ps      - viewer is for ps\n",
   "   -view=pdf     - viewer is for pdf\n",
+  "   -xelatex      - use xelatex for processing files to pdf\n",
+  "\n",
   "   filename = the root filename of LaTeX document\n",
   "\n",
   "-p, -pv and -pvc are mutually exclusive\n",
   "-h, -c and -C override all other options.\n",
   "-pv and -pvc require one and only one filename specified\n",
   "All options can be introduced by '-' or '--'.  (E.g., --help or -help.)\n",
-  "Contents of RC file specified by -r overrides options specified\n",
-  "  before the -r option on the command line\n";
+  " \n",
+  "In addition, latexmk recognizes many other options that are passed to\n",
+  "latex and/or pdflatex without interpretation by latexmk.  Run latexmk\n",
+  "with the option -showextraoptions to see a list of these\n";
 
 } #END print_help
 
@@ -2902,9 +3374,14 @@
 
 sub check_biber_log {
     # Check for biber warnings:
-    # Usage: check_biber_log( base_of_biber_run[, \@biber_source )
-    # return 0: OK, 1: biber warnings, 2: biber errors, 
-    #        3: could not open .blg file.
+    # Usage: check_biber_log( base_of_biber_run, \@biber_source )
+    # return 0: OK;
+    #        1: biber warnings;
+    #        2: biber errors;
+    #        3: could not open .blg file;
+    #        4: failed to find one or more source files, except for bibfile;
+    #        5: failed to find bib file;
+    #        6: missing file, one of which is control file
     #       10: only error is missing \citation commands.
     # Side effect: add source files @biber_source
     my $base = $_[0];
@@ -2917,52 +3394,82 @@
     my $have_error = 0;
     my $missing_citations = 0;
     my $no_citations = 0;
-    my $error_count = 0;
-    my $warning_count = 0;
+    my $error_count = 0;            # From my counting of error messages
+    my $warning_count = 0;          # From my counting of warning messages
+    # The next two occur only from biber
+    my $bibers_error_count = 0;     # From biber's counting of errors
+    my $bibers_warning_count = 0;   # From biber's counting of warnings
+    my $not_found_count = 0;
+    my $control_file_missing = 0;
     while (<$log_file>) {
         if (/> WARN /) { 
             print "Biber warning: $_"; 
             $have_warning = 1;
             $warning_count ++;
         }
-        elsif (/> FATAL /) {
+        elsif (/> (FATAL|ERROR) /) {
             print "Biber error: $_"; 
-            $have_error = 1;
-            $error_count ++;
-            if ( /> FATAL - The file '[^']+' does not contain any citations!/ ) {
-                $no_citations++;
+            if ( /> (FATAL|ERROR) - Cannot find file '([^']+)'/    #'
+                 || /> (FATAL|ERROR) - Cannot find '([^']+)'/ ) {  #'
+                $not_found_count++;
+                push @$Pbiber_source, $2;
+            }
+            elsif ( /> (FATAL|ERROR) - Cannot find control file '([^']+)'/ ) {  #'
+                $not_found_count++;
+                $control_file_missing = 1;
+                push @$Pbiber_source, $2;
+            }
+            else {
+                $have_error = 1;
+                $error_count ++;
+                if ( /> (FATAL|ERROR) - The file '[^']+' does not contain any citations!/ ) { #'
+                    $no_citations++;
+	        }
             }
         }
         elsif ( /> INFO - Found .* '([^']+)'\s*$/
                 || /> INFO - Found '([^']+)'\s*$/
+                || /> INFO - Reading '([^']+)'\s*$/
+                || /> INFO - Reading (.*)$/
                 || /> INFO - Processing .* file '([^']+)' .*$/
               ) {
 	    if ( defined $Pbiber_source ) {
                 push @$Pbiber_source, $1;
 	    }
         }
+        elsif ( /> INFO - WARNINGS: ([\d]+)\s*$/ ) {
+            $bibers_warning_count = $1;
+	}
+        elsif ( /> INFO - ERRORS: ([\d]+)\s*$/ ) {
+            $bibers_error_count = $1;
+	}
     }
     close $log_file;
-    my $bibret = &find_file_list1( $Pbiber_source, $Pbiber_source,
-                                  '', \@BIBINPUTS );
+
+    my @not_found = &find_file_list1( $Pbiber_source, $Pbiber_source,
+                                      '', \@BIBINPUTS );
     @$Pbiber_source = uniqs( @$Pbiber_source );
-    if ($bibret == 0) {
-        warn "$My_name: Found biber source file(s) [@$Pbiber_source]\n" 
+    if ( ($#not_found < 0) && ($#$Pbiber_source >= 0) ) {
+        warn "$My_name: Found biber source file(s) [@$Pbiber_source]\n"
         unless $silent;
     }
+    elsif ( ($#not_found == 0) && ($not_found[0] =~ /\.bib$/) ) {
+        # Special treatment if sole missing file is bib file
+        # I don't want to treat that as an error
+        warn "$My_name: Biber did't find bib file [$not_found[0]]\n";
+	return 5;
+    }
     else {
-        warn "$My_name: Failed to find one or more biber source files ",
-             "in [@$Pbiber_source]\n";
+        show_array( "$My_name: Failed to find one or more biber source files:",
+                    @not_found );
         if ($force_mode) {
             warn "==== Force_mode is on, so I will continue.  ",
                  "But there may be problems ===\n";
         }
-        else {
-            #$failure = -1;
-            #$failure_msg = 'Failed to find one or more biber source files';
-            #warn "$My_name: Failed to find one or more biber source files\n";
-        }
-        return 3;
+        if ($control_file_missing) {
+            return 6;
+	}
+        return 4;
     }
 #    print "$My_name: #Biber errors = $error_count, warning messages = $warning_count,\n  ",
 #          "missing citation messages = $missing_citations, no_citations = $no_citations\n";
@@ -2979,12 +3486,49 @@
 
 #**************************************************
 
+sub run_bibtex {
+    my $return = 999;
+    if ( $aux_dir ) {
+        if ( $$Psource =~ /^$aux_dir1/ ) {
+            # Run bibtex in $aux_dir, fixing input search path
+            # to allow for finding files in original directory
+            my ( $base, $path, $ext ) = fileparseA( $$Psource );
+            my $cwd = good_cwd();
+            foreach ( 'BIBINPUTS', 'BSTINPUTS' ) {
+	        if ( exists $ENV{$_} ) {
+    	            $ENV{$_} = $cwd.$search_path_separator.$ENV{$_};
+	        }
+	        else {
+		    $ENV{$_} = $cwd.$search_path_separator;
+		}
+	    }
+            pushd( $path );
+            $return = &Run_subst( undef, undef, '', $base.$ext, '', $base );
+            popd();
+        }
+        else {
+            warn "$My_name: Directory in file name '$$Psource' for bibtex\n",
+                 "   but it is not the output directory '$aux_dir'\n";
+            $return = Run_subst();
+	}
+    }
+    else {
+        $return = Run_subst();
+    }
+    return $return;
+}
+
+
+#**************************************************
+
 sub check_bibtex_log {
     # Check for bibtex warnings:
     # Usage: check_bibtex_log( base_of_bibtex_run )
     # return 0: OK, 1: bibtex warnings, 2: bibtex errors, 
     #        3: could not open .blg file.
-    #       10: only error is missing \citation commands.
+    #       10: only error is missing \citation commands or a missing aux file
+    #           (which would normally be corrected after a later run of 
+    #           (pdf)latex).
 
     my $base = $_[0];
     my $log_name = "$base.blg";
@@ -2994,27 +3538,41 @@
     my $have_warning = 0;
     my $have_error = 0;
     my $missing_citations = 0;
+    my @missing_aux = ();
     my $error_count = 0;
     while (<$log_file>) {
         if (/^Warning--/) { 
             #print "Bibtex warning: $_"; 
             $have_warning = 1;
         }
+        elsif ( /^I couldn\'t open auxiliary file (.*\.aux)/ ) {
+            push @missing_aux, $1;
+	}
         elsif ( /^I found no \\citation commands---while reading file/ ) {
-            $missing_citations++; 
+            $missing_citations++;
 	}
-        elsif (/There (were|was) (\d+) error message/) { 
+        elsif (/There (were|was) (\d+) error message/) {
             $error_count = $2;
             #print "Bibtex error: count=$error_count $_"; 
             $have_error = 1;
         }
     }
     close $log_file;
-    #print "Bibtex errors = $error_count, missing citations = $missing_citations\n";
-    if ($have_error && ($error_count <= $missing_citations ) 
-        && ($missing_citations > 0) ) {
-        # If the only error is a missing citation line, that should only 
+    my $missing = $missing_citations + $#missing_aux + 1;
+
+    if ( $#missing_aux > -1 ) {
+        # Need to make the missing files.
+        warn "$My_name: One or more aux files is missing for bibtex. I'll try\n",
+             "          to get (pdf)latex to remake them.\n";
+        rdb_for_some( [keys %current_primaries], sub{ $$Pout_of_date = 1; } );
+    }
+    #print "Bibtex errors = $error_count, missing aux files and citations = $missing\n";
+    if ($have_error && ($error_count <= $missing )
+        && ($missing > 0) ) {
+        # If the only error is a missing citation line, that should only
         # count as a warning.
+        # Also a missing aux file should be innocuous; it will be created on
+        # next run of (pdf)latex.  ?? HAVE I HANDLED THAT CORRECTLY?
         # But have to deal with the problem that bibtex gives a non-zero 
         # exit code.  So leave things as they are so that the user gets
         # a better diagnostic ??????????????????????????
@@ -3029,26 +3587,25 @@
 
 #**************************************************
 
-sub clean_file_name {
-    # Convert quoted filename as found in log file to filename without quotes
-    # Allows arbitrarily embedded double-quoted substrings, includes the
-    # cases
-    # 1. `"string".ext', which arises e.g., from \jobname.bbl:
-    #    when the base filename contains spaces, \jobname has quotes.
-    #    and from \includegraphics with basename specified.
-    #    Also deals with filenames written by asymptote.sty
-    # 2. Or "string.ext" from \includegraphcs with basename and ext specified.
-    #    and from MiKTeX logfile for input files with spaces. 
-    # Doubled quotes (e.g., A""B) don't get converted.
-    # Neither do unmatched quotes.
-    my $filename = $_[0];
-    while ( $filename =~ s/^([^\"]*)\"([^\"]+)\"(.*)$/$1$2$3/ ) {}
-    return $filename;
-}
+sub normalize_force_directory {
+    #  Usage, normalize_force_directory( dir, filename )
+    #  Perform the following operations:
+    #    Clean filename
+    #    If filename contains no path component, insert dir in front
+    #    Normalize filename
+    #  Return result
+    my $default_dir = $_[0];
+    my $filename = clean_filename( $_[1] );
+    my ($base_name, $path ) = fileparse( $filename );
+    if ( $base_name eq $filename ) {
+       $filename = "$default_dir$filename";
+    }
+    return normalize_filename( $filename );
+} #END normalize force_directory
 
 # ------------------------------
 
-sub parse_logB {
+sub parse_log {
 # Scan log file for: dependent files
 #    reference_changed, bad_reference, bad_citation
 # Return value: 1 if success, 0 if no log file.
@@ -3109,7 +3666,6 @@
     $bad_reference = 0;
     $bad_citation = 0;
 
-    my $log_name = "$root_filename.log";
     my $log_file = new FileHandle;
     if ( ! open( $log_file, "<$log_name" ) ) {
         return 0;
@@ -3188,8 +3744,9 @@
 	        # First line OK
                 next LINE;
             } else {
-                warn "$My_name: Error on first line of '$log_name'.  ".
-                    "This is apparently not a TeX log file.\n";
+                warn "$My_name: Error on first line of '$log_name'.\n".
+                    "This is apparently not a TeX log file.  ",
+		    "The first line is:\n$_\n";
                 $failure = 1;
                 $failure_msg = "Log file '$log_name' appears to have wrong format.";
                 return 0;
@@ -3202,7 +3759,7 @@
                 if ( ($block_type eq 'conversion') 
                      && /^\($current_pkg\)\s+Output file: <([^>]+)>/ ) 
                 {
-		    $delegated_output = $1;
+		    $delegated_output = normalize_clean_filename($1);
                 }
 		next LINE;
 	    }
@@ -3216,20 +3773,20 @@
 	}
         # Check for changed references, bad references and bad citations:
         if (/Rerun to get/) { 
-            warn "$My_name: References changed.\n";
+            warn "$My_name: References changed.\n" if ! $silent;
             $reference_changed = 1;
         } 
 	if (/LaTeX Warning: (Reference[^\001]*undefined)./) { 
-	    warn "$My_name: $1 \n";
-	    $bad_reference = 1;
+	    warn "$My_name: $1 \n" unless $silent;
+	    $bad_reference++;
 	} 
 	if (/LaTeX Warning: (Citation[^\001]*undefined)./) {
-	    warn "$My_name: $1 \n";
-	    $bad_citation = 1;
+	    warn "$My_name: $1 \n" unless $silent;
+	    $bad_citation++;
 	}
         if (/Package natbib Warning: (Citation[^\001]*undefined)./) {
-            warn "$My_name: $1 \n";
-            $bad_citation = 1;
+            warn "$My_name: $1 \n" unless $silent;
+            $bad_citation++;
 	}
 	if ( /^Document Class: / ) {
 	    # Class sign-on line
@@ -3245,7 +3802,7 @@
 	    next LINE;
 	}
 	if ( /^Output written on\s+(.*)\s+\(\d+\s+page/ ) {
-            $primary_out = clean_file_name($1);
+            $primary_out = normalize_clean_filename($1);
 	    warn "$My_name: Log file says output to '$primary_out'\n"
 	       unless $silent;
 	    next LINE;
@@ -3259,15 +3816,18 @@
 	    next LINE;
 	}
         if ( /^\\openout\d+\s*=\s*\`([^\']+)\'\.$/ ) {
-            $generated_log{clean_file_name($1)} = 1;
+                #  When (pdf)latex is run with an -output-directory 
+                #    or an -aux_directory, the file name does not contain
+                #    the output path; fix this, after removing quotes:
+            $generated_log{normalize_force_directory( $aux_dir1, $1 )} = 1;
 	    next LINE;
 	}
         # Test for conversion produced by package:
 	if ( /^Package (\S+) Info: Source file: <([^>]+)>/ ) {
 	    # Info. produced by epstopdf (and possibly others) 
             #    about file conversion
-            $current_pkg = clean_file_name($1);
-            $delegated_source = clean_file_name($2);
+            $current_pkg = normalize_clean_filename($1);
+            $delegated_source = normalize_clean_filename($2);
             $block_type = 'conversion';
 	    next LINE;
 	}
@@ -3294,9 +3854,12 @@
    		     "  '$_'\n";
                 next LINE;
 	    }
-	    # Typically, there is trailing space, not part of filename:
+	        # Typically, there is trailing space, not part of filename:
 	    $idx_file =~ s/\s*$//;
-	    $idx_file = clean_file_name($idx_file);
+                #  When (pdf)latex is run with an -output-directory 
+                #    or an -aux_directory, the file name does not contain
+                #    the output path; fix this, after removing quotes:
+	    $idx_file = normalize_force_directory( $aux_dir1, $idx_file );
 	    my ($idx_base, $idx_path, $idx_ext) = fileparseA( $idx_file );
 	    $idx_base = $idx_path.$idx_base;
             $idx_file = $idx_base.$idx_ext;
@@ -3320,8 +3883,10 @@
 	    next LINE;
 	}
 	if ( /^No file (.*?\.bbl)./ ) {
-	    # Notice that the
-	    my $bbl_file = clean_file_name($1);
+                #  When (pdf)latex is run with an -output-directory 
+                #    or an -aux_directory, the file name does not contain
+                #    the output path; fix this, after removing quotes:
+	    my $bbl_file = normalize_force_directory( $aux_dir1, $1 );
 	    warn "$My_name: Non-existent bbl file '$bbl_file'\n $_\n";
     	    $dependents{$bbl_file} = 0;
 	    push @bbl_files, $bbl_file;
@@ -3329,16 +3894,28 @@
 	}
 	foreach my $pattern (@file_not_found) {
 	    if ( /$pattern/ ) {
-		my $file = clean_file_name($1);
+                my $file = clean_filename($1);
 		warn "$My_name: Missing input file: '$file' from line\n  '$_'\n"
 		    unless $silent;
-		$dependents{$file} = 0;
+		$dependents{normalize_filename($file)} = 0;
+		my $file1 = $file;
+                if ( $aux_dir ) {
+                      # Allow for the possibility that latex generated
+                      # a file in $aux_dir, from which the missing file can
+                      # be created by a cusdep (or other) rule that puts
+                      # the result in $out_dir.  If the announced missing file
+                      # has no path, then it would be effectively a missing
+                      # file in $aux_dir, with a path.  So give this alternate
+                      # location.
+                      my $file1 = normalize_force_directory( $aux_dir1, $file );
+		      $dependents{$file1} = 0;
+		}
 		next LINE;
 	    }
 	}
 	if ( /^File: (.+) Graphic file \(type / ) {
 	    # First line of message from includegraphics/x
-	    $dependents{clean_file_name($1)} = 1;
+	    $dependents{normalize_clean_filename($1)} = 1;
 	    next LINE;
 	}
 	# Now test for generic lines to ignore, only after special cases!
@@ -3467,6 +4044,7 @@
 	    }
 	INCLUDE_NAME:
             foreach my $include_name (@new_includes) {
+                $include_name = normalize_filename( $include_name );
 	        my ($base, $path, $ext) = fileparseB( $include_name );
                 if ( ($path eq './') || ($path eq '.\\') ) {
                     $include_name = $base.$ext;
@@ -3654,23 +4232,45 @@
         }
     }
     return 1;
-} #END parse_logB
+} #END parse_log
 
 #************************************************************
 
 sub parse_fls {
-    my ($fls_name, $Pinputs, $Poutputs ) = @_;
-    %$Pinputs = %$Poutputs = ();
+    my ($fls_name, $Pinputs, $Poutputs, $Pfirst_read_after_write ) = @_;
+    %$Pinputs = %$Poutputs = %$Pfirst_read_after_write = ();
     my $fls_file = new FileHandle;
+    # Make a note of current working directory
+    # I'll update it from the fls file later
+    # Currently I don't use this, but it would be useful to use
+    # this when testing prefix for cwd in a filename, by
+    # giving (pdf)latex's best view of the cwd.  Note that the
+    # value given by the cwd() function may be mangled, e.g., by cygwin
+    # compared with native MSWin32.
+    my $cwd = good_cwd();
     if ( ! open ($fls_file, "<$fls_name") ) {
         return 1;
     }
     foreach $_ ( <$fls_file> ) {
-        if (/^\s*INPUT\s+(.*)\s+$/) {
-	    $$Pinputs{$1} = 1;
+        # Remove trailing CR and LF. Thus we get correct behavior when an fls file
+        #  is produced by MS-Windows program (e.g., in MiKTeX) with CRLF line ends,
+        #  but is read by Unix Perl (which treats LF as line end, and preserves CRLF
+        #  in read-in lines):
+        $_ =~ s/[\n\r]*$//;
+        if (/^\s*PWD\s+(.*)$/) {
+            $cwd = $1;
+        }
+        elsif (/^\s*INPUT\s+(.*)$/) {
+            # Take precautions against aliasing of foo, ./foo and other possibilities for cwd.
+            my $file = normalize_filename( $1 );
+            if ( (exists $$Poutputs{$file}) && (! exists $$Pinputs{$file}) ) {
+                $$Pfirst_read_after_write{$file} = 1;
+            }
+	    $$Pinputs{$file} = 1;
 	}
-        elsif (/^\s*OUTPUT\s+(.*)\s+$/) {
-	    $$Poutputs{$1} = 1;
+        elsif (/^\s*OUTPUT\s+(.*)$/) {
+            # Take precautions against aliasing of foo, ./foo and other possibilities for cwd.
+	    $$Poutputs{ normalize_filename( $1 )} = 1;
 	}
     }
     close( $fls_file );
@@ -3679,6 +4279,68 @@
 
 #************************************************************
 
+sub clean_filename {
+    # Convert quoted filename as found in log file to filename without quotes
+    # Allows arbitrarily embedded double-quoted substrings, includes the
+    # cases
+    # 1. `"string".ext', which arises e.g., from \jobname.bbl:
+    #    when the base filename contains spaces, \jobname has quotes.
+    #    and from \includegraphics with basename specified.
+    #    Also deals with filenames written by asymptote.sty
+    # 2. Or "string.ext" from \includegraphcs with basename and ext specified.
+    #    and from MiKTeX logfile for input files with spaces. 
+    # Doubled quotes (e.g., A""B) don't get converted.
+    # Neither do unmatched quotes.
+    my $filename = $_[0];
+    while ( $filename =~ s/^([^\"]*)\"([^\"]+)\"(.*)$/$1$2$3/ ) {}
+    return $filename;
+}
+
+# ------------------------------
+
+sub normalize_filename {
+   # Remove various forms for cwd at start of filename.
+   # Convert to have directory separator = '/' only
+   my $file = $_[0];
+   my $file1 = $file;   # Saved original value
+   my $cwd = good_cwd();
+   # Normalize files to use / to separate directory components:
+   # (Note both / and \ are allowed under MSWin.)
+   $cwd =~ s(\\)(/)g;
+   $file =~ s(\\)(/)g;
+
+   # Remove current directory string:
+   $file =~ s(^\./)();
+   $file =~ s(^$cwd/)();
+
+   return $file;
+}
+
+# ------------------------------
+
+sub normalize_clean_filename {
+    # Remove quotes around filename --- see clean_filename --- as from log file.
+    # Then remove any string for cwd, and convert to use '/' for directory separator,
+    # (and any other standardization) done by normalize_filename.
+    return normalize_filename( clean_filename( $_[0] ));
+}
+
+#************************************************************
+
+sub OS_preferred_filename {
+   # Usage: OS_preferred_filename(name)
+   # Returns filename with directory separator '/' converted
+   # to preferred conventions for current OS.
+   # Currently implemented: only '\' for MSWin32
+   my $file = $_[0];
+   if ( $^O eq 'MSWin32' ) {
+      $file =~ s(/)(\\)g;
+    }
+   return $file;
+}
+
+#************************************************************
+
 sub parse_aux {
     #Usage: parse_aux( $aux_file, \@new_bib_files, \@new_aux_files, \@new_bst_files )
     # Parse aux_file (recursively) for bib files, and bst files.  
@@ -3712,18 +4374,18 @@
         warn "$My_name: No .bib files listed in .aux file '$aux_file' \n",
         return 2;
     }
-    my $bibret = &find_file_list1( $Pbib_files, $Pbib_files,
-                                  '.bib', \@BIBINPUTS );
+    my @not_found = &find_file_list1( $Pbib_files, $Pbib_files,
+                                      '.bib', \@BIBINPUTS );
     @$Pbib_files = uniqs( @$Pbib_files );
     &find_file_list1( $Pbst_files, $Pbst_files, '.bst' );
     @$Pbst_files = uniqs( @$Pbst_files );
-    if ($bibret == 0) {
-        warn "$My_name: Found bibliography file(s) [@$Pbib_files]\n" 
+    if ( $#not_found < 0) {
+        warn "$My_name: Found bibliography file(s) [@$Pbib_files]\n"
         unless $silent;
     }
     else {
-        warn "$My_name: Failed to find one or more bibliography files ",
-             "in [@$Pbib_files]\n";
+        show_array( "$My_name: Failed to find one or more bibliography files ",
+                    @not_found );
         if ($force_mode) {
             warn "==== Force_mode is on, so I will continue.  ",
                  "But there may be problems ===\n";
@@ -3771,7 +4433,7 @@
       }
       elsif ( /^\\\@input\{(.*)\}/ ) { 
           # \\@input{next_aux_file_name}
-	  &parse_aux1( $1 );
+	  &parse_aux1( $aux_dir1.$1 );
       }
    }
    close($aux_fh);
@@ -3789,11 +4451,12 @@
 #************************************************************
 
 sub fdb_get {
-    # Call: fdb_get(filename [, run_time])
+    # Call: fdb_get(filename [, check_time])
     # Returns an array (time, size, md5) for the current state of the
     #    named file.
-    # The optional argument run_time is the runtime of some command
-    #    associated with the use of the file --- see below.
+    # The optional argument check_time is either the run_time of some command
+    #    that may have changed the file or the last time the file was checked
+    #    for changes --- see below.
     # For non-existent file, deletes its entry in fdb_current, 
     #    and returns (0,-1,0)  
     # As an optimization, the md5 value is taken from the cache in 
@@ -3811,11 +4474,11 @@
     #    at some runtime t, the file is rewritten later by the same or another
     #    program, with timestamp t, and when the initial file also has 
     #    timestamp t.
-    # A test is applied for this situation if the run_time argument is 
+    # A test is applied for this situation if the check_time argument is
     #    supplied and is nonzero.
 
-    my ($file, $run_time) = @_;
-    if ( ! defined $run_time ) { $run_time = 0;}
+    my ($file, $check_time) = @_;
+    if ( ! defined $check_time ) { $check_time = 0;}
     my ($new_time, $new_size) = get_time_size($file);
     my @nofile =  (0,-1,0);     # What we use for initializing
 				# a new entry in fdb or flagging
@@ -3833,23 +4496,27 @@
     my $file_data = $fdb_current{$file};
     my ( $time, $size, $md5 ) = @$file_data;
 
-#warn "--------- Getting MD5: $file: (N,O,R) = $new_time, $time, $run_time\n";
-#warn "--------- $file: (OT,OS,OM) = @$file_data\n";
     if ( ($new_time != $time) || ($new_size != $size) 
-         || ( $run_time && ($run_time == $time ) )
+         || ( $check_time && ($check_time == $time ) )
        ) {
-        # Only force recalculation of md5 if time or size changed
-        # Or if the time equals run_time, so that the file may
-        #   have changed within the 1-second granularity of the time
+        # Only force recalculation of md5 if time or size changed.
+        # However, the physical file time may have changed without
+        #   affecting the value of the time coded in $time, because
+        #   times are computed with a 1-second granularity.
+        #   The only case to treat specially is where the file was created,
+        #   then used by the current rule, and then rewritten, all within
+        #   the granularity size, otherwise the value of the reported file
+        #   time changed, and we've handled it.  But we may have already
+        #   checked this at an earlier time than the current check.  So the
+        #   only dangerous case is where the file time equals a check_time,
+        #   which is either the run_time of the command or the time of a
+        #   previous check.
         # Else we assume file is really unchanged.
         $recalculate_md5 = 1;
     }
     if ($recalculate_md5) {
-#warn "--------- RECALC MD5: $rule $file: (N,O,R) = $new_time, $time, $run_time\n";
-#warn "  ------- $file: (OT,OS,OM) = @$file_data\n";
-#&traceback;
+#warn "--------- RECALC MD5: $rule $file: (N,O,R,C) \n  = $new_time, $time, $$Prun_time, $check_time\n";
         @$file_data = ( $new_time, $new_size, get_checksum_md5( $file ) );
-#warn "  ------- $file: (NT,NS,NM) = @$file_data\n";
     }
     return @$file_data;;
 } #END fdb_get
@@ -3926,7 +4593,7 @@
 	    $rule = $1;
             my $tail = $'; #'  Single quote in comment tricks the parser in
                            # emacs from misparsing an isolated single quote
-            $run_time = 0;
+            $run_time = $check_time = 0;
             $source = $dest = $base = '';
             if ( $tail =~ /^\s*(\S+)\s*$/ ) {
                 $run_time = $1;
@@ -3937,13 +4604,19 @@
                 $dest = $3;
                 $base = $4;
 	    }
+            elsif ( $tail =~ /^\s*(\S+)\s+\"([^\"]*)\"\s+\"([^\"]*)\"\s+\"([^\"]*)\"\s+(\S+)\s*$/ ) {
+                $run_time = $1;
+                $source = $2;
+                $dest = $3;
+                $base = $4;
+                $check_time = $5;
+	    }
             if ( rdb_rule_exists( $rule ) ) {
                 rdb_one_rule( $rule, 
-                              sub{ $$Ptest_kind = 1; 
+                              sub{ 
+                                   if ($$Ptest_kind == 3) { $$Ptest_kind = 1; }
                                    $$Prun_time = $run_time;
-                                   #??if ($source) { $$Psource = $source; }
-                                   #??if ($dest) { $$Pdest = $dest; }
-                                   #??if ($base) { $$Pbase = $base; }
+                                   $$Pcheck_time = $check_time;
                                  }                                      
                              );
 	    }
@@ -3965,11 +4638,12 @@
                 # If it existed on last run, it will be in later 
                 #    lines of the fdb file
                 rdb_create_rule( $rule, 'cusdep', '', $PAnew_cmd, 1, 
-                                 $source, $dest, $base, 0, $run_time, 1 );
+                                 $source, $dest, $base, 0, $run_time, $check_time, 1 );
 	    }
             elsif ( $rule =~ /^(makeindex|bibtex|biber)\s*(.*)$/ ) {
                 my $PA_extra_gen = [];
                 my $rule_generic = $1;
+                my $int_cmd = '';
                 if ( ! $source ) {
                     # If fdb_file was old-style (v. 1)
                     $source = $2;
@@ -3991,18 +4665,20 @@
 	        }
                 if ($rule =~ /^makeindex/) { $PA_extra_gen = [ "$base.ilg" ]; }
                 if ($rule =~ /^(bibtex|biber)/) { $PA_extra_gen = [ "$base.blg" ]; }
+                if ($rule =~ /^bibtex/) { $int_cmd = "run_bibtex"; }
   	        warn "$My_name: File-database '$in_name': setting rule '$rule'\n"
                    if $diagnostics;
                 my $cmd_type = 'external';
                 my $ext_cmd = ${$rule_generic};
 		warn "  Rule kind = '$rule_generic'; ext_cmd = '$ext_cmd';\n",
+                     "  int_cmd = '$int_cmd';\n",
 		     "  source = '$source'; dest = '$dest'; base = '$base';\n"
                    if $diagnostics;
                 # Set source file as non-existent.  
                 # If it existed on last run, it will be in later 
                 #    lines of the fdb file
-                rdb_create_rule( $rule, $cmd_type, $ext_cmd, '', 1, 
-                                 $source, $dest, $base, 0, $run_time, 1, $PA_extra_gen );
+                rdb_create_rule( $rule, $cmd_type, $ext_cmd, $int_cmd, 1, 
+                                 $source, $dest, $base, 0, $run_time,  $check_time, 1, $PA_extra_gen );
 	    }
             else {
   	        warn "$My_name: In file-database '$in_name' rule '$rule'\n",
@@ -4059,7 +4735,7 @@
     }
     undef $in_handle;
     # Set cus dependencies.
-    &rdb_set_dependentsA( keys %rule_db );
+    &rdb_set_dependents( keys %rule_db );
 
 #?? Check from_rules exist.
 
@@ -4112,7 +4788,7 @@
            { 
                return; 
            }
-           print $out_handle "[\"$rule\"] $$Prun_time \"$$Psource\" \"$$Pdest\" \"$$Pbase\" \n"; 
+           print $out_handle "[\"$rule\"] $$Prun_time \"$$Psource\" \"$$Pdest\" \"$$Pbase\" $$Pcheck_time\n";
            rdb_do_files(
              sub { print $out_handle "  \"$file\" $$Ptime $$Psize $$Pmd5 \"$$Pfrom_rule\"\n"; }
 	   );
@@ -4155,6 +4831,9 @@
     local %generated_log = (); # Lists generated files found in log file
     local %generated_fls = (); # Lists generated files found in fls file
     local %source_fls = ();    # Lists source files found in fls file
+    local %first_read_after_write = (); # Lists source files that are only read
+                                  # after being written (so are not true
+                                  # source files.
     local $primary_out = $$Pdest;  # output file (dvi or pdf)
     local %conversions = ();   # (pdf)latex-performed conversions.
                      # Maps output file created and read by (pdf)latex
@@ -4162,14 +4841,15 @@
     # The following are also returned, but are global, to be used by caller
     # $reference_changed, $bad_reference $bad_citation
 
-    &parse_logB;
-    my $fls_file = "$root_filename.fls";
+    &parse_log;
+    my $fls_file = "$aux_dir1$root_filename.fls";
     if ($recorder && test_gen_file($fls_file) ) {
-        parse_fls( $fls_file, \%source_fls, \%generated_fls );
+        parse_fls( $fls_file, \%source_fls, \%generated_fls, \%first_read_after_write );
         foreach (keys %source_fls) {
             $dependents{$_} = 4;
 	}
         foreach (keys %generated_fls) {
+            $_ = normalize_filename($_);
             rdb_add_generated( $_ );
             if ( exists($dependents{$_}) ) {
                $dependents{$_} = 6;
@@ -4185,7 +4865,7 @@
     #         missing input file might be correctable by a run of some
     #         other program whose running is provoked AFTER a run of
     #         (pdf)latex, we'll set a diagnostic and leave it to the
-    #         rdb_makeB to handle after all circular dependencies are
+    #         rdb_make to handle after all circular dependencies are
     #         resolved. 
     #   2.  The output file might be of a different kind than expected
     #         (i.e., dvi instead of pdf, or vv).  This could
@@ -4209,9 +4889,9 @@
             print "!!!===Creating rule '$from_rule': '$ind_file' from '$idx_file'\n"
                   if ($diagnostics);
             rdb_create_rule( $from_rule, 'external', $makeindex, '', 1, 
-                             $idx_file, $ind_file, $ind_base, 1, 0);
+                             $idx_file, $ind_file, $ind_base, 1, 0, 0 );
             print "  ===Source file '$ind_file' for '$rule'\n"
-                  if ($diagnostics > -1);
+                  if ($diagnostics);
             rdb_ensure_file( $rule, $ind_file, $from_rule );
 	}
         # Make sure the .ind file is treated as a detected source file;
@@ -4255,11 +4935,11 @@
             print "   ===Creating rule '$from_rule'\n" if ($diagnostics);
             if ( $bib_program eq 'biber' ) {
                 rdb_create_rule( $from_rule, 'external', $biber, '', 1,
-                                 "$bbl_base.bcf", $bbl_file, $bbl_base, 1, 0);
+                                 "$bbl_base.bcf", $bbl_file, $bbl_base, 1, 0, 0 );
 	     }
              else {
-                 rdb_create_rule( $from_rule, 'external', $bibtex, '', 1,
-                                  "$bbl_base.aux", $bbl_file, $bbl_base, 1, 0);
+                 rdb_create_rule( $from_rule, 'external', $bibtex, 'run_bibtex', 1,
+                                  "$bbl_base.aux", $bbl_file, $bbl_base, 1, 0, 0 );
 	       }
 	}
         local %old_sources = ();
@@ -4331,7 +5011,7 @@
         }
     }
 
-    my @more_sources = &rdb_set_dependentsA( $rule );
+    my @more_sources = &rdb_set_dependents( $rule );
     my $num_new = $#more_sources + 1;
     foreach (@more_sources) { 
 	$dependents{$_} = 4;
@@ -4342,6 +5022,9 @@
             $$Pchanged = 1; # New files can be made.  Ignore error.
         }
     }
+    foreach (keys %first_read_after_write) {
+        delete $dependents{$_};
+    }
     if ($diagnostics) {
 	if ($num_new > 0 ) {
 	    print "$num_new new source files for rule '$rule':\n";
@@ -4350,6 +5033,13 @@
 	else {
 	    print "No new source files for rule '$rule':\n";
 	}
+        my @first_read_after_write = sort keys %first_read_after_write;
+        if ($#first_read_after_write >= 0) {
+            print "The following files were only read after being written:\n";
+            foreach (@first_read_after_write) {
+                print "   '$_'\n";
+	    }
+	  }
     }
     my @files_not_needed = ();
     foreach (keys %$PHsource) { 
@@ -4383,8 +5073,8 @@
 
 #************************************************************
 
-sub rdb_find_new_filesB {
-    # Call: rdb_find_new_filesB
+sub rdb_find_new_files {
+    # Call: rdb_find_new_files
     # Assumes rule context for primary rule.
     # Deal with files which were missing and for which a method
     # of finding them has become available:
@@ -4476,30 +5166,30 @@
 	}
     }
     return $found;
-} # END rdb_find_new_filesB
+} # END rdb_find_new_files
 
 #************************************************************
 
-sub rdb_set_dependentsA {
-    # Call rdb_set_dependentsA( rules ...)
+sub rdb_set_dependents {
+    # Call rdb_set_dependents( rules ...)
     # Returns array (sorted), of new source files.
     local @new_sources = ();
     local @deletions = ();
 
 # Shouldn't recurse.  The definite rules to be examined are given.
-    rdb_for_some( [@_],  0, \&rdb_one_depA );
-# OLD    rdb_recurseA( [@_],  0, \&rdb_one_depA );
+    rdb_for_some( [@_],  0, \&rdb_one_dep );
+# OLD    rdb_recurse( [@_],  0, \&rdb_one_dep );
     foreach (@deletions) {
 	my ($rule, $file) = @$_;
         rdb_remove_files( $rule, $file );
     }
     &rdb_make_links;
     return uniqs( @new_sources );
-} #END rdb_set_dependentsA
+} #END rdb_set_dependents
 
 #************************************************************
 
-sub rdb_one_depA {
+sub rdb_one_dep {
     # Helper for finding dependencies.  One case, $rule and $file given
     # Assume file (and rule) context for DESTINATION file.
 
@@ -4508,7 +5198,7 @@
     if ( (! exists $possible_primaries{$rule}) && ($rule !~ /^cusdep/) ) {
         return;
     }
-#print "=============ONE_DEPA: '$rule' '$file'\n";
+#print "=============ONE_DEP: '$rule' '$file'\n";
     local $new_dest = $file;
     my ($base_name, $path, $toext) = fileparseA( $new_dest );
     $base_name = $path.$base_name;
@@ -4580,7 +5270,7 @@
                 local @PAnew_cmd = ( 'do_cusdep', $func_name );
                 if (! rdb_rule_exists( $from_rule ) ) {
                     rdb_create_rule( $from_rule, 'cusdep', '', \@PAnew_cmd, 3, 
-                                     $source, $new_dest, $base_name, 0);
+                                     $source, $new_dest, $base_name, 0 );
 		}
                 else {
 		    rdb_one_rule( 
@@ -4600,10 +5290,9 @@
         # Try to make the missing file
         #Set character to surround filenames in commands:
         my $q = $quote_filenames ? '"' : '';
-	if ($rule =~ /^cusdep/ ) { traceback(); }
         if ( $toext ne '' ) {
              print "$My_name: '$rule': source file '$file' doesn't exist. I'll try making it...\n";
-             &Run_msg( "$make $q$file$q" );
+             &Run_subst( "$make $q$file$q" );
              if ( -e $file ) {
                  return;
 	     }
@@ -4613,7 +5302,7 @@
                    "   I'll try making it with allowed extensions \n";
              foreach my $try_ext ( keys %$Pinput_extensions ) {
                  my $new_dest = "$file.$try_ext";
-                 &Run_msg( "$make $q$new_dest$q" );
+                 &Run_subst( "$make $q$new_dest$q" );
                  if ( -e $new_dest ) {
                      print "SUCCESS in making '$new_dest'\n";
                      # Put file in rule, without a from_rule, but
@@ -4631,7 +5320,7 @@
 	   }
 	}
     }
-} #END rdb_one_depA
+} #END rdb_one_dep
 
 #************************************************************
 
@@ -4688,13 +5377,24 @@
         delete $source{$_};
     }
     foreach my $dest (@dest) {
-       print $fh "$root_filename$dest :";
+       if ($deps_file eq '-' ) {
+          print $fh "$root_filename$dest :";
+       } else {
+          print $fh "$root_filename$dest $deps_file :";
+       }
        foreach (sort keys %source) {
            print $fh "\\\n    $_";
        }
        print $fh "\n";
     }
     print $fh "#===End dependents for $filename:\n";
+    if ($dependents_phony) {
+        print $fh "\n#===Phony rules for $filename:\n\n";
+        foreach (sort keys %source) {
+            print $fh "$_ :\n\n";
+        }
+        print $fh "#===End phony rules for $filename:\n";
+    }
 } #END deps_list
 
 #************************************************************
@@ -4726,7 +5426,7 @@
     # Call: rdb_accessible( rule, ...)
     # Returns array of rules accessible from the given rules
     local @accessible = ();
-    rdb_recurseA( [@_], sub{ push @accessible, $rule; } );
+    rdb_recurse( [@_], sub{ push @accessible, $rule; } );
     return @accessible;
 } #END rdb_accessible
 
@@ -4734,8 +5434,8 @@
 #************************************************************
 #************************************************************
 
-sub rdb_makeB {
-    # Call: rdb_makeB( target, ... )
+sub rdb_make {
+    # Call: rdb_make( target, ... )
     # Makes the targets and prerequisites.  
     # Leaves one-time rules to last.
     # Does appropriate repeated makes to resolve dependency loops
@@ -4895,7 +5595,7 @@
     local $failure = 0;        # General accumulated error flag
     local $missing_dvi_pdf = ''; # Did primary run fail to make its output file? 
     local $runs = 0;
-    local $too_many_runs = 0;
+    local $too_many_passes = 0;
     local %rules_applied = ();
     my $retry_msg = 0;         # Did I earlier say I was going to attempt 
                                # another pass after a failure?
@@ -4906,6 +5606,7 @@
         }
       PASS:
         while (1==1) {
+            # Exit condition at end of body of loop.
             $runs = 0;
             my $previous_failure = $failure;
             $failure = 0;
@@ -4916,25 +5617,20 @@
 	    if ($diagnostics) {
                 print "MakeB: doing pre_primary and primary...\n";
             }
-            rdb_for_some( [@pre_primary, $primary], \&rdb_makeB1 );
-            if ( ($runs > 0) && ! $too_many_runs ) {
-                $retry_msg = 0;
-                if ( $failure && $newrule_nofile ) { 
-                    $retry_msg = 1;
-                    print "$My_name: Error on run, but found possibility to ",
-                          "make new source files\n";
-                    next PASS;
-		}
-                elsif ( $force_mode || (! $failure) ) {
-                    next PASS;
-		}
+            # Do the primary run if it is needed. On return $runs == 0
+            #       signals that nothing was run (and hence no output
+            #       files changed), either because no input files
+            #       changed and no run was needed, or because the
+            #       number of passes through the rule exceeded the
+            #       limit.  In the second case $too_many_runs is set.
+            rdb_for_some( [@pre_primary, $primary], \&rdb_make1 );
+            if ( ($runs > 0) && ! $too_many_passes ) {
+                next PASS;
             }
-            elsif ($runs == 0) {
+            if ($runs == 0) {
                 # $failure not set on this pass, so use value from previous pass:
                 $failure = $previous_failure;
-                if ($retry_msg) {
-                    print "But in fact no new files made\n";
-		}
+                if ($failure && !$force_mode ) { last PASS; }
 	    }
             if ( $missing_dvi_pdf ) { 
                # No output from primary, after completing circular dependence
@@ -4942,15 +5638,16 @@
                $failure = 1; 
                last PASS;
             }    
-            if ($failure && !$force_mode ) { last PASS; }
 	    if ($diagnostics) {
   	        print "MakeB: doing post_primary...\n";
 	    }
-            rdb_for_some( [@post_primary], \&rdb_makeB1 );
-            if ($failure) { last PASS; }
-            if ($runs > 0) { next PASS; }
-            # Get here if nothing was run.
-            last PASS;
+            rdb_for_some( [@post_primary], \&rdb_make1 );
+            if ( ($runs == 0) || $too_many_passes ) {
+                # If $too_many_passes is set, it should also be that
+                # $runs == 0; but for safety, I also checked
+                # $too_many_passes.
+                last PASS;
+	    }
 	}
 	continue {
             # Re-evaluate rule classification and accessibility,
@@ -4962,18 +5659,11 @@
             &rdb_make_links;
 	}
     }
-    rdb_for_some( [@one_time], \&rdb_makeB1 );
-    rdb_write( $fdb_file );
+    rdb_for_some( [@one_time], \&rdb_make1 );
+    rdb_write( $fdb_name );
 
-    if (! $silent) { 
-        # Diagnose of the runs
-        if ( $#{keys %rules_applied }  > -1 ) {
-            print "$My_name: $runs runs.  Rules applied:\n";
-            foreach (sort keys %rules_applied) {
-		print "    '$_'\n";
-	    }
-	}
-	elsif ($failure && $force_mode) {
+    if (! $silent) {
+	if ($failure && $force_mode) {
             print "$My_name: Errors, in force_mode: so I tried finishing targets\n";
 	}
 	elsif ($failure) {
@@ -4986,43 +5676,54 @@
 	}
     }
     return $failure;
-} #END rdb_makeB
+} #END rdb_make
 
 #-------------------
 
 sub rdb_show_rule_errors {
-    local @messages = ();
+    local @errors = ();
+    local @warnings = ();
     rdb_for_all( 
 	       sub{
 		   if ($$Plast_message ne '') {
-		       push @messages, "$rule: $$Plast_message";
+                       if ($$Plast_result == 200) {
+   		          push @warnings, "$rule: $$Plast_message";
+		       }
+		       else {
+		          push @errors, "$rule: $$Plast_message";
+		       }
 		   }
 		   elsif ($$Plast_result == 1) {
-		       push @messages, "$rule: failed to create output file";
+		       push @errors, "$rule: failed to create output file";
 		   }
 		   elsif ($$Plast_result == 2) {
-		       push @messages, "$rule: gave an error";
+		       push @errors, "$rule: gave an error";
 		   }
 		   elsif ($$Prun_time == 0) {
-#    This can have innocuous causes.  So don't report
-#		       push @messages, "$rule: never run";
+                       #  This can have innocuous causes.  So don't report
 		   }
 	       }
 	      );
-    if ($#messages > -1) { 
+    if ($#warnings > -1) { 
+	warn "Collected warning summary (may duplicate other messages):\n";
+	foreach (@warnings){
+	    warn "  $_\n";
+	}
+    }
+    if ($#errors > -1) { 
 	warn "Collected error summary (may duplicate other messages):\n";
-	foreach (@messages){
+	foreach (@errors){
 	    warn "  $_\n";
 	}
     }
-    return $#messages+1;
+    return $#errors+1;
 }
 
 #-------------------
 
-sub rdb_makeB1 {
-    # Call: rdb_makeB1
-    # Helper routine for rdb_makeB.
+sub rdb_make1 {
+    # Call: rdb_make1
+    # Helper routine for rdb_make.
     # Carries out make at level of given rule (all data available).
     # Assumes contexts for recursion, make, and rule, and
     # assumes that source files for the rule are to be considered
@@ -5081,8 +5782,15 @@
 	    #      not run the rule, but not set an error condition.
 	    #      Any error will arise at the (pdf)latex level due to a 
 	    #      missing source file at that level.
-	    if ( ( $$Pcmd_type eq 'cusdep') && $$Psource && (! -e $$Psource) ) {
-		# No action
+	    if ( $$Psource && (! -e $$Psource)
+# OLD                && ( ( $$Pcmd_type eq 'cusdep') )
+# NEW
+                 && ( ( $$Pcmd_type ne 'primary') )
+               ) {
+                # Main source file doesn't exist, and rule is NOT primary.
+		# No action, since a run is pointless.  Primary is different:
+                # file might be found elsewhere (by kpsearch from (pdf)latex),
+                # while non-existence of main source file is a clear error.
 	    }
 	    elsif ( $$Pcmd_type eq 'delegated' ) {
 		# Delegate to destination rule
@@ -5111,9 +5819,6 @@
         &rdb_diagnose_changes( "Rule '$rule': " );
     }
 
-    $rules_applied{$rule} = 1;
-    $runs++;
-
     # We are applying the rule, so its source file state for when it
     # was last made is as of now:
     # ??IS IT CORRECT TO DO NOTHING IN CURRENT VERSION?
@@ -5127,15 +5832,17 @@
         # Getting here represents some kind of weird error.
         warn "$My_name: Maximum runs of $rule reached ",
              "without getting stable files\n";
-        warn "     Use the -f option to force complete processing.\n"
-            if (! $force_mode);
-        $too_many_runs = 1;
+        $too_many_passes = 1;
         # Treat rule as completed, else in -pvc mode get infinite reruns:
         $$Pout_of_date = 0;
         $failure = 1;
 	$failure_msg = "'$rule' needed too many passes";
         return;
     }
+
+    $rules_applied{$rule} = 1;
+    $runs++;
+
     $pass{$rule}++; 
     if ($bibtex_not_run > 0) {
         if ($bibtex_not_run == 1 ) {
@@ -5150,7 +5857,7 @@
     else {
         warn_running( "Run number $pass{$rule} of rule '$rule'" );
         if ($$Pcmd_type eq 'primary' ) { 
-            $return = &rdb_primary_run; 
+            $return = &rdb_primary_run;
         }
         else { $return = &rdb_run1; }
     }
@@ -5180,14 +5887,18 @@
             # For a primary rule, i.e., (pdf)latex, not to produce the 
             #    expected output file may not be an error condition.  
             # Diagnostics were handled in parsing the log file.
-            # Special action in main loop inrdb_makeB1
+            # Special action in main loop in rdb_make
             $missing_dvi_pdf = $$Pdest;
         }
+        elsif ($return == -2) {
+           # Missing output file was reported to be NOT an error
+           $$Pout_of_date = 0;
+	}
 	else {
             $failure = 1;
 	}
     }
-    if ($return != 0) {
+    if ( ($return != 0) && ($return != -2) ) {
         $failure = 1; 
 	$$Plast_result = 2;
         if ( !$$Plast_message ) {
@@ -5196,24 +5907,22 @@
 # !!??        $failure_msg = $$Plast_message;
         
     }
-}  #END rdb_makeB1
-
-#************************************************************
-
-sub rdb_submakeB {
-    # Call: rdb_submakeB
-    # Makes all the source files for a given rule.
-    # Assumes contexts for recursion, for make, and rule.
-    %visited = %visited_at_rule_start;
-    local $failure = 0;  # Error flag
-    my @v = keys %visited;
-#??    print "---submakeB $rule.  @v \n";
-    rdb_do_files( sub{ rdb_recurse_rule( $$Pfrom_rule, 0,0,0, \&rdb_makeB1 ) } );
-    return $failure;
-}  #END rdb_submakeB
-
-#************************************************************
-
+}  #END rdb_make1
+
+#************************************************************
+
+#??sub rdb_submake {
+#??    # Call: rdb_submake
+#??    # Makes all the source files for a given rule.
+#??    # Assumes contexts for recursion, for make, and rule.
+#??    %visited = %visited_at_rule_start;
+#??    local $failure = 0;  # Error flag
+#??    my @v = keys %visited;
+#??    rdb_do_files( sub{ rdb_recurse_rule( $$Pfrom_rule, 0,0,0, \&rdb_make1 ) } );
+#??    return $failure;
+#??}  #END rdb_submake
+
+#************************************************************
 
 sub rdb_classify_rules {
     # Usage: rdb_classify_rules( \%allowed_primaries, requested targets )
@@ -5238,7 +5947,7 @@
     @post_primary = ();
     @one_time = ();
 
-    rdb_recurseA( \@requested_targets, \&rdb_classify1, 0,0, \&rdb_classify2 );
+    rdb_recurse( \@requested_targets, \&rdb_classify1, 0,0, \&rdb_classify2 );
 
     # Reverse, as tendency is to find last rules first.
     @pre_primary = reverse @pre_primary;
@@ -5327,11 +6036,13 @@
     # Assumes contexts for: rule.
     # Unconditionally apply the rule
     # Returns return code from applying the rule.
-    # Otherwise: 0 on other kind of success, -1 on error.
+    # Otherwise: 0 on other kind of success, 
+    #            -1 on error, 
+    #            -2 when missing dest_file is to be ignored
 
-    # Source file data, by definition, correspond to the file state just before 
-    # the latest run, and the run_time to the time just before the run:
-    &rdb_update_filesA;
+    # Source file data, by definition, correspond to the file state just
+    # before the latest run, and the run_time to the time just before the run:
+    &rdb_update_files;
     $$Prun_time = time;
     $$Pchanged = 0;       # No special changes in files
     $$Plast_result = 0;
@@ -5352,7 +6063,7 @@
         $return = &$int_cmd( @int_args ); 
     }
     elsif ($$Pext_cmd) {
-	$return = &rdb_ext_cmd;
+	$return = &Run_subst();
     }
     else {
         warn "$My_name: Either a bug OR a configuration error:\n",
@@ -5363,8 +6074,35 @@
         $$Plast_message = "Bug or configuration error; incorrect command type";
     }
     if ( $rule =~ /^biber/ ) {
-        my $retcode = check_biber_log($$Pbase);
-        if ($retcode == 3) {
+        my @biber_source = ( );
+        my $retcode = check_biber_log( $$Pbase, \@biber_source );
+        foreach my $source ( @biber_source ) {
+            print "  === Source file '$source' for '$rule'\n"
+               if ($diagnostics);
+            rdb_ensure_file( $rule, $source );
+        }
+        if ($retcode == 5) {
+        # Special treatment if sole missing file is bib file
+        # I don't want to treat that as an error
+            $return = 0;
+            $$Plast_result = 200;
+            $$Plast_message = "Could not find bib file for '$$Pbase'";
+            push @warnings, "Bib file not found for '$$Pbase'";
+        }
+        elsif ($retcode == 6) {
+           # Missing control file.  Need to remake it (if possible)
+           # Don't treat missing bbl file as error.
+           warn "$My_name: bibtex control file missing.  Since that can\n",
+                "   be recreated, I'll try to do so.\n";
+           $return = -2;
+           rdb_for_some( [keys %current_primaries], sub{ $$Pout_of_date = 1; } );
+	}
+        elsif ($retcode == 4) {
+            $$Plast_result = 2;
+            $$Plast_message = "Could not find all biber source files for '$$Pbase'";
+            push @warnings, "Not all biber source files found for '$$Pbase'";
+        }
+        elsif ($retcode == 3) {
             $$Plast_result = 2;
             $$Plast_message = "Could not open biber log file for '$$Pbase'";
             push @warnings, $$Plast_message;
@@ -5378,13 +6116,16 @@
         }
         elsif ($retcode == 10) {
             push @warnings, "Biber found no citations for '$$Pbase'";
-            # Biber doesn't generate a bbl file in this situation.  So I cannot
-            #   ignore the error the way I do with bibtex.
-            #$return = 0;
+            # Biber doesn't generate a bbl file in this situation.
+            $return = -2;
         }
     }
     if ( $rule =~ /^bibtex/ ) {
         my $retcode = check_bibtex_log($$Pbase);
+        if ( ! -e $$Psource ) {
+            $retcode = 10;
+            rdb_for_some( [keys %current_primaries], sub{ $$Pout_of_date = 1; } );
+	}
         if ($retcode == 3) {
             $$Plast_result = 2;
             $$Plast_message = "Could not open bibtex log file for '$$Pbase'";
@@ -5392,15 +6133,23 @@
         }
         elsif ($retcode == 2) {
             $$Plast_message = "Bibtex errors: See file '$$Pbase.blg'";
+            $failure = 1;
             push @warnings, $$Plast_message;
         }
         elsif ($retcode == 1) {
             push @warnings, "Bibtex warnings for '$$Pbase'";
         }
         elsif ($retcode == 10) {
-            push @warnings, "Bibtex found no citations for '$$Pbase'";
-            # But this is an innocuous error, so fix return code
-            $return = 0;
+            push @warnings, "Bibtex found no citations for '$$Pbase',\n",
+                            "    or bibtex found a missing aux file\n";
+            if (! -e $$Pdest ) {
+                warn "$My_name: Bibtex did not produce '$$Pdest'.  But that\n",
+                     "     was because of missing files, so I will continue.\n";
+                $return = -2;
+	    }
+            else {
+                $return = 0;
+	    }
         }
     }
 
@@ -5412,16 +6161,15 @@
     }
     $$Pout_of_date = $$Pout_of_date_user = 0;
 
-    if ( ($$Plast_result == 0) && ($return != 0) ) {
+    if ( ($$Plast_result == 0) && ($return != 0) && ($return != -2) ) {
         $$Plast_result = 2;
         if ($$Plast_message eq '') {
 	    $$Plast_message = "Command for '$rule' gave return code $return";
 	}
     }
-    elsif ( $$Pdest && (! -e $$Pdest) ) {
+    elsif ( $$Pdest && (! -e $$Pdest) && ($return != -2) ) {
 	$$Plast_result = 1;
     }
-
     return $return;
 }  # END rdb_run1
 
@@ -5435,7 +6183,7 @@
 
     # Source file data, by definition, correspond to the file state just before 
     # the latest run, and the run_time to the time just before the run:
-    &rdb_update_filesA;
+    &rdb_update_files;
     $$Prun_time = time;
     $$Pchanged = 0;       # No special changes in files
     $$Plast_result = 0;
@@ -5453,41 +6201,59 @@
 
 #-----------------
 
-sub rdb_ext_cmd {
-    # Call: rdb_ext_cmd
-    # Assumes rule context.  Runs external command with substitutions.
-    # Uses defaults for the substitutions.  See rdb_ext_cmd1.
-    return rdb_ext_cmd1();
-} #END rdb_ext_cmd
-