latexmk 4.27a (18oct11)

git-svn-id: svn://tug.org/texlive/trunk@24326 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 308 insertions, 132 deletions

diff --git a/Master/texmf-dist/scripts/latexmk/latexmk.pl b/Master/texmf-dist/scripts/latexmk/latexmk.pl
index d0a41d5d76e..2bceb1e803d 100755
--- a/Master/texmf-dist/scripts/latexmk/latexmk.pl
+++ b/Master/texmf-dist/scripts/latexmk/latexmk.pl
@@ -1,4 +1,9 @@
 #!/usr/bin/env perl
+
+## ????????????????????? biber source file issue fatal or not: 
+## Check generation of retcode 4, and ITS USE, which is source of latexmk stop.
+
+
 # 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
@@ -22,6 +27,7 @@ use warnings;
 ## (I have hooks for this).
 
 
+
 #=======================================
 
 #??  Force mode doesn't appear to do force (if error in latex file)
@@ -107,8 +113,8 @@ use warnings;
 
 $my_name = 'latexmk';
 $My_name = 'Latexmk';
-$version_num = '4.26';
-$version_details = "$My_name, John Collins, 9 August 2011";
+$version_num = '4.27a';
+$version_details = "$My_name, John Collins, 10 October 2011";
 
 
 use Config;
@@ -177,6 +183,26 @@ else {
 ##
 ##   Modification log from 1 Jan 2011 onwards in detail
 ##
+##     10 Oct 2011, John Collins  Corrections to new options:
+##                                Substitutions in commands
+##                                Locate .fls correctly
+##      9 Oct 2011, John Collins  Add options -aux-directory -output-directory
+##      2 Oct 2011, John Collins  Parse summary of warnings and errors from 
+##                                  biber v. 0.9.6
+##      1 Oct 2011, John Collins  Add -norc option that prevents auto reading
+##                                  of rc files.
+##                                The lines adding (or not) 'bbl' to
+##                                  @generated_exts: move them to after parsing
+##                                  of command line options, so that they can
+##                                  respect setting of $bibtex_use from command
+##                                  line options.
+##     20 Sep 2011, John Collins  Add png to list of graphics extensions for
+##                                  pdflatex
+##     23 Aug 2011, John Collins  Warning about making view file via temporary
+##                                Deal with the case that the command for
+##                                  making the view file has no %D placeholder
+##                                Version 4.27
+##     15 Aug 2011, John Collins  Missing file error in biber non-fatal
 ##      9 Aug 2011, John Collins  Fix bug in error reporting by check_biber_log
 ##                                Handle log file from biber 0.9.4
 ##      7 Jul 2011, John Collins  Fix process_rc_file to evade cygwin bug.
@@ -383,7 +409,7 @@ $pdflatex_silent_switch  = '-interaction=batchmode';
 #        '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' );
 
 ## Command to invoke biber & bibtex
@@ -473,7 +499,7 @@ $log_file_binary = 0;   # Whether to treat log file as binary
 $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
@@ -783,6 +809,7 @@ else {
 }
 
 ## 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 
@@ -838,6 +865,10 @@ $jobname = '';          # Jobname: as with current tex, etc indicates
                         # 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.
@@ -1101,7 +1132,8 @@ if (!$TEXINPUTS) { $TEXINPUTS = '.'; }
                     #       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 $out_dir1
                     #     int_cmd specifies any internal command to be
 		    #       used to implement the application of the
 		    #       rule.  If this is present, it overrides
@@ -1161,7 +1193,7 @@ if (!$TEXINPUTS) { $TEXINPUTS = '.'; }
                     #     default_extra_generated is a reference to an array
                     #       of specifications of extra generated files (beyond
                     #       the main dest file.  Standard place holders are used.
-                    #       Example ['%R.log'] for (pdf)latex, and ['%R.blg'] 
+                    #       Example ['%Y%R.log'] for (pdf)latex, and ['%R.blg'] 
                     #          for bibtex.  (There's no need for '%R.aux', here,
                     #          since such generated files are detected dynamically.)
                     #   1: {Hash sourcefile -> [source-file data] }
@@ -1199,9 +1231,6 @@ if (!$TEXINPUTS) { $TEXINPUTS = '.'; }
 %fdb_current = ();  # Fdb-hash for all files used.
 
 
-#==================================================
-## Read rc files:
-
 # User's home directory
 $HOME = '';
 if (exists $ENV{'HOME'} ) {
@@ -1212,6 +1241,21 @@ elsif (exists $ENV{'USERPROFILE'} ) {
 }
 
 
+#==================================================
+
+# Options that are to be obeyed before rc files are read:
+
+foreach $_ ( @ARGV )
+{
+    # Make -- and - equivalent at beginning of option:
+    s/^--/-/;
+    if (/^-norc$/ ) {
+        $auto_rc_use = 0;
+    }
+}
+
+#==================================================
+## Read rc files with this subroutine
 
 sub read_first_rc_file_in_list {
     foreach my $rc_file ( @_ ) {
@@ -1224,33 +1268,35 @@ sub read_first_rc_file_in_list {
     }
 }
 
-# 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';
+# 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" );
 }
-
-#show_array ("BIBINPUTS", @BIBINPUTS); die;
 
 ## 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 ($_ = $ARGV[0])
 {
   # Make -- and - equivalent at beginning of option:
   s/^--/-/;
   shift;
-  if (/^-bibtex$/) { $bibtex_use = 2; }
+  if ( /^-aux-directory=(.*)$/ || /^-auxdir=(.*)$/ ) {
+      $aux_dir = $1;
+  }
+  elsif (/^-bibtex$/) { $bibtex_use = 2; }
   elsif (/^-bibtex-$/) { $bibtex_use = 0; }
   elsif (/^-nobibtex$/) { $bibtex_use = 0; }
   elsif (/^-bibtex-cond$/) { $bibtex_use = 1; }
@@ -1267,6 +1313,7 @@ while ($_ = $ARGV[0])
       $deps_file = $1;
       $dependents_list = 1; 
   }
+  elsif (/^-diagnostics/) { $diagnostics = 1; }
   elsif (/^-dvi$/)   { $dvi_mode = 1; }
   elsif (/^-dvi-$/)  { $dvi_mode = 0; }
   elsif (/^-f$/)     { $force_mode = 1; }
@@ -1277,7 +1324,6 @@ while ($_ = $ARGV[0])
      $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 = $1;
   }
@@ -1286,24 +1332,31 @@ while ($_ = $ARGV[0])
   elsif (/^-latex=(.*)$/) {
       $latex = $1;
   }
-  elsif (/^-pdflatex=(.*)$/) {
-      $pdflatex = $1;
-  }
   elsif (/^-new-viewer$/) {
-                       $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
                        $preview_mode = 0;  
                      }
   elsif (/^-p-$/)    { $printout_mode = 0; }
-  elsif (/^-pdfdvi$/){ $pdf_mode = 3; }
-  elsif (/^-pdfps$/) { $pdf_mode = 2; }
   elsif (/^-pdf$/)   { $pdf_mode = 1; }
   elsif (/^-pdf-$/)  { $pdf_mode = 0; }
+  elsif (/^-pdfdvi$/){ $pdf_mode = 3; }
+  elsif (/^-pdflatex=(.*)$/) {
+      $pdflatex = $1;
+  }
+  elsif (/^-pdfps$/) { $pdf_mode = 2; }
   elsif (/^-print=(.*)$/) {
       $value = $1;
       if ( $value =~ /^dvi$|^ps$|^pdf$/ ) {
@@ -1334,12 +1387,12 @@ while ($_ = $ARGV[0])
   elsif (/^-silent$/ || /^-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 $version_num\n";
+      exit;
+  }
   elsif (/^-verbose$/)  { $silent = 0; }
   elsif (/^-view=default$/) { $view = "default";}
   elsif (/^-view=dvi$/)     { $view = "dvi";}
@@ -1417,6 +1470,23 @@ warn "$My_name: This is $version_details, version: $version_num.\n",
      "**** Report bugs etc to John Collins <collins at phys.psu.edu>. ****\n"
    unless $silent;
 
+if ( ($out_dir ne '') && ($aux_dir eq '') ){
+    $aux_dir = $out_dir;
+}
+
+# Versions terminating in directory/path separator
+$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 $texfile_search is initialized to "", a nonzero value indicates
 # that an initialization file has set it.
@@ -1540,8 +1610,8 @@ if ( ($jobname ne '') && ($num_files > 1) ) {
 &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 );
 
 
 # If landscape mode, change dvips processor, and the previewers:
@@ -1553,23 +1623,32 @@ if ( $landscape_mode )
 }
 
 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( "$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 ( $aux_dir && ($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 ( $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?
@@ -1620,7 +1699,7 @@ if ( $banner ) { $requested_filerules{'dvips'} = 1; }
 
 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.
@@ -1704,26 +1783,29 @@ foreach $filename ( @file_list )
         $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.
     %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(
@@ -1748,7 +1830,7 @@ foreach $filename ( @file_list )
         }
         else {
             # No fdb file, so do inferior job by parse_logB
-            print "$My_name: Examining log file '$root_filename.log' for generated files...\n";
+            print "$My_name: Examining log file '$log_name' for generated files...\n";
 
             # Variables set by parse_logB. Can I remove them
             local %generated_log = ();
@@ -1790,8 +1872,7 @@ foreach $filename ( @file_list )
                        ." (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 
                  );
@@ -1805,12 +1886,12 @@ foreach $filename ( @file_list )
 	    &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 $fdb_name; }
     if ($cleanup_only) { next FILE; }
 
 
@@ -1840,7 +1921,7 @@ foreach $filename ( @file_list )
     }
 
     $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.
@@ -1848,8 +1929,8 @@ foreach $filename ( @file_list )
         &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) { 
@@ -1860,7 +1941,7 @@ foreach $filename ( @file_list )
 	rdb_recurseA( [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 );
 	}
     }
@@ -2000,10 +2081,14 @@ sub fix_cmds {
 #############################################################
 
 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
 
 #############################################################
@@ -2011,17 +2096,18 @@ sub add_option {
 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 $print_file = '';
@@ -2061,14 +2147,14 @@ sub rdb_make_rule_list {
 # This is because, especially for dvi file, the contents of the file may contain
 #    a pointer to a file to be included, not the contents of the file! 
     %rule_list = (
-        'latex'    => [ 'primary',  "$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',   $view_file,  "",        "",   2 ],
@@ -2109,6 +2195,8 @@ sub rdb_set_rules {
 	    # until run time, in case of changes.
 	    foreach ($base, $source, $dest, @$PA_extra_gen ) {
 		s/%R/$root_filename/;
+		s/%Y/$aux_dir1/;
+		s/%Z/$out_dir1/;
 	    }
 	    foreach ($source, $dest ) { 
 		s/%B/$base/;
@@ -2170,20 +2258,20 @@ sub set_trivial_aux_fdb {
     # 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
 
 #************************************************************
@@ -2252,12 +2340,22 @@ sub do_viewfile {
     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 = &rdb_ext_cmd1( '', '', $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 = &rdb_ext_cmd;
+	}
     }
     else {
         $return = &rdb_ext_cmd;
+        $return = &rdb_ext_cmd;
     }
     return $return;
 } #END do_viewfile
@@ -2674,9 +2772,10 @@ sub execute_code_string {
 #************************************************************
 
 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/;
+        (my $name = /%R/ ? $_ : "%R.$_") =~ s/%R/$dir$root_filename/;
         unlink("$name");
     }
 } #END cleanup1
@@ -2792,9 +2891,12 @@ sub print_help
   "$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",
@@ -2839,6 +2941,9 @@ sub print_help
   "   -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",
@@ -2860,6 +2965,8 @@ sub print_help
   "            (Side effect: turn off ordinary preview mode.)\n",
   "   -pvc-  - turn off -pvc\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",
@@ -2883,9 +2990,7 @@ sub print_help
   "-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";
+  "All options can be introduced by '-' or '--'.  (E.g., --help or -help.)\n";
 
 } #END print_help
 
@@ -2937,12 +3042,13 @@ sub view_file_via_temporary {
 
 sub check_biber_log {
     # Check for biber warnings:
-    # Usage: check_biber_log( base_of_biber_run[, \@biber_source )
+    # 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;
+    #        4: failed to find one or more source files, except for bibfile;
+    #        5: failed to find bib file;
     #       10: only error is missing \citation commands.
     # Side effect: add source files @biber_source
     my $base = $_[0];
@@ -2955,8 +3061,12 @@ sub check_biber_log {
     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 v > 
+    my $bibers_error_count = 0;     # From biber's counting of errors
+    my $bibers_warning_count = 0;   # From biber's counting of warnings
+    my $not_found_count = 0;
     while (<$log_file>) {
         if (/> WARN /) { 
             print "Biber warning: $_"; 
@@ -2965,10 +3075,16 @@ sub check_biber_log {
         }
         elsif (/> FATAL /) {
             print "Biber error: $_"; 
-            $have_error = 1;
-            $error_count ++;
-            if ( /> FATAL - The file '[^']+' does not contain any citations!/ ) {
-                $no_citations++;
+            if ( /> FATAL - Cannot find file '([^']+)'/ ) {  #'
+                $not_found_count++;
+                push @$Pbiber_source, $1;
+            }
+            else {
+                $have_error = 1;
+                $error_count ++;
+                if ( /> FATAL - The file '[^']+' does not contain any citations!/ ) { #'
+                    $no_citations++;
+	        }
             }
         }
         elsif ( /> INFO - Found .* '([^']+)'\s*$/
@@ -2981,6 +3097,12 @@ sub check_biber_log {
                 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;
 
@@ -2988,9 +3110,15 @@ sub check_biber_log {
                                       '', \@BIBINPUTS );
     @$Pbiber_source = uniqs( @$Pbiber_source );
     if ( $#not_found < 0) {
-        warn "$My_name: Found biber source file(s) [@$Pbiber_source]\n" 
+        warn "$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 {
         show_array( "$My_name: Failed to find one or more biber source files:",
                     @not_found );
@@ -2998,11 +3126,6 @@ sub check_biber_log {
             warn "==== Force_mode is on, so I will continue.  ",
                  "But there may be problems ===\n";
         }
-        else {
-            #$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 4;
     }
 #    print "$My_name: #Biber errors = $error_count, warning messages = $warning_count,\n  ",
@@ -3070,6 +3193,21 @@ sub check_bibtex_log {
 
 #**************************************************
 
+sub force_directory {
+    #  Usage, force_directory( dir, filename )
+    #  If filename contains no path component, return concatenation
+    #     of dir and filename,
+    #  else return filename
+    my $default_dir = $_[0];
+    my $filename = $_[1];
+    my ($base_name, $path ) = fileparse( $filename );
+    if ( $path ne '' ) { $filename = "$default_dir$filename"; }
+    print "$filename\n";
+    return $filename;
+}
+
+# ------------------------------
+
 sub clean_file_name {
     # Convert quoted filename as found in log file to filename without quotes
     # Allows arbitrarily embedded double-quoted substrings, includes the
@@ -3150,7 +3288,6 @@ sub parse_logB {
     $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;
@@ -3300,7 +3437,10 @@ LINE:
 	    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{ force_directory( $aux_dir1, clean_file_name($1) )} = 1;
 	    next LINE;
 	}
         # Test for conversion produced by package:
@@ -3335,9 +3475,12 @@ LINE:
    		     "  '$_'\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 = force_directory( $aux_dir1, clean_file_name($idx_file) );
 	    my ($idx_base, $idx_path, $idx_ext) = fileparseA( $idx_file );
 	    $idx_base = $idx_path.$idx_base;
             $idx_file = $idx_base.$idx_ext;
@@ -3361,8 +3504,10 @@ LINE:
 	    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 = force_directory( $aux_dir1, clean_file_name($1) );
 	    warn "$My_name: Non-existent bbl file '$bbl_file'\n $_\n";
     	    $dependents{$bbl_file} = 0;
 	    push @bbl_files, $bbl_file;
@@ -4018,6 +4163,7 @@ LINE:
                     my $ext = '';
                     ($base, $path, $ext) = fileparseA( $source );
                     $base = $path.$base;
+# ?? MAY NEED TO FIX THE FOLLOWING IF $aux_dir IS SET.
                     if ($rule_generic eq 'makeindex') {
                         $dest = "$base.ind";
 		    }
@@ -4204,7 +4350,7 @@ sub rdb_set_latex_deps {
     # $reference_changed, $bad_reference $bad_citation
 
     &parse_logB;
-    my $fls_file = "$root_filename.fls";
+    my $fls_file = "$aux_dir1$root_filename.fls";
     if ($recorder && test_gen_file($fls_file) ) {
         parse_fls( $fls_file, \%source_fls, \%generated_fls );
         foreach (keys %source_fls) {
@@ -4288,6 +4434,7 @@ sub rdb_set_latex_deps {
             rdb_remove_rule( "bibtex $bbl_base" );
         }
         else {
+# ?? MAY NEED TO FIX IF $aux_dir IS SET:
             parse_aux( "$bbl_base.aux", \@new_bib_files, \@new_aux_files, \@new_bst_files );
             # Remove OPPOSITE kind of bbl generation:
             rdb_remove_rule( "biber $bbl_base" );
@@ -4722,6 +4869,7 @@ sub deps_list {
 	sub{ $source{$file} = 1; }
     );
     foreach (keys %generated_exts_all) {
+# ?? MAY NEED TO FIX THE FOLLOWING IF $aux_dir or $out_dir IS SET.
         (my $name = /%R/ ? $_ : "%R.$_") =~ s/%R/$root_filename/;
         push @generated, $name;
     }
@@ -5008,7 +5156,7 @@ sub rdb_makeB {
 	}
     }
     rdb_for_some( [@one_time], \&rdb_makeB1 );
-    rdb_write( $fdb_file );
+    rdb_write( $fdb_name );
 
     if (! $silent) { 
         # Diagnose of the runs
@@ -5415,7 +5563,16 @@ sub rdb_run1 {
                if ($diagnostics);
             rdb_ensure_file( $rule, $source );
         }
-        if ($retcode == 4) {
+        if ($retcode == 5) {
+        # Special treatment if sole missing file is bib file
+        # I don't want to treat that as an error
+	    warn " =============== bib missing special case\n";
+#            $return = 0;
+            $$Plast_result = 200;
+#            $$Plast_message = "Could not find bib file for '$$Pbase'";
+            push @warnings, "Bib file not found for '$$Pbase'";
+        }
+        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'";
@@ -5522,7 +5679,8 @@ sub rdb_ext_cmd1 {
     # Call: rdb_ext_cmd1( options, source, dest, base ) or rdb_ext_cmd1() or ...
     # Assumes rule context.  Returns command with substitutions.
     # Null arguments or unprovided arguments => use defaults.
-    # for %S=source, %D=dest, %B=base, %R=root=base for latex, %O='', %T=texfile
+    # for %S=source, %D=dest, %B=base, %R=root=base for latex, %O='', 
+    # %T=texfile, %Y for $aux_dir1, %Z for $out_dir1
     my ($options, $source, $dest, $base ) = @_;
     # Apply defaults
     $options ||= '';
@@ -5542,6 +5700,8 @@ sub rdb_ext_cmd1 {
        '%T' => $q.$texfile_name.$q,
        '%S' => $q.$source.$q,
        '%D' => $q.$dest.$q,
+       '%Y' => $q.$aux_dir1.$q,
+       '%Z' => $q.$out_dir1.$q,
        '%%' => '%'         # To allow literal %B, %R, etc, by %%B.
     );
 
@@ -5573,28 +5733,44 @@ sub rdb_primary_run {
     if (-e $$Pdest) { $missing_dvi_pdf = '';}
 
     ######### Analyze results of run:
-    if ( ! -e "$root_filename.log" ) {
+    if ( ! -e $log_name ) {
         $failure = 1;
         $$Plast_result = 2;
-        $$Plast_message = $failure_msg = "(Pdf)LaTeX failed to generate a log file";
+        $$Plast_message = $failure_msg 
+           = "(Pdf)LaTeX failed to generate the expected log file '$log_name'";
         return -1;
     }
 
     if ($recorder) {
         # Handle problem that some version of (pdf)latex give fls files
-        # of name latex.fls or pdflatex.fls instead of $root_filename.fls:
-        my $std_fls_file = "$root_filename.fls";
-        my $other_fls_file = "latex.fls";
+        #    of name latex.fls or pdflatex.fls instead of $root_filename.fls.
+        # Also that setting of -output-directory -aux-directory is not 
+        #    respected by (pdf)latex, at least in some versions.
+        my $std_fls_file = "$aux_dir1$root_filename.fls";
+        my @other_fls_names = ( );
         if ( $rule =~ /^pdflatex/ ) {
-            $other_fls_file = "pdflatex.fls";
+            push @other_fls_names, "pdflatex.fls";
+	}
+        else {
+            push @other_fls_names, "latex.fls";
 	}
+        if ( $aux_dir1 ne '' ) {
+           push @other_fls_names, "$root_filename.fls";
+	}
+        my $have_fls = 0;
         if ( test_gen_file($std_fls_file) ) {
-             # Good filename
+             $have_fls = 1;
 	}
-        elsif ( test_gen_file($other_fls_file) ) {
-            copy $other_fls_file, $std_fls_file;
-        }
         else {
+            foreach my $cand (@other_fls_names) {
+                if ( test_gen_file($cand) ) {
+                    copy $cand, $std_fls_file;
+                    $have_fls = 1;
+                    last;
+		}
+	    }
+        }
+        if (! $have_fls) {
             warn "$My_name: fls file doesn't appear to have been made\n";
 	}
     }