diff --git a/Configurations/common.tmpl b/Configurations/common.tmpl
index cdcaf5320f..af1746a144 100644
--- a/Configurations/common.tmpl
+++ b/Configurations/common.tmpl
@@ -42,8 +42,11 @@
      my $bin = shift;
      my %opts = @_;
      if ($unified_info{generate}->{$src}) {
+         my $script = $unified_info{generate}->{$src}->[0];
          $OUT .= generatesrc(src => $src,
                              generator => $unified_info{generate}->{$src},
+                             generator_incs => $unified_info{includes}->{$script},
+                             generator_deps => $unified_info{depends}->{$script},
                              deps => $unified_info{depends}->{$src},
                              incs => [ @{$unified_info{includes}->{$bin}},
                                        @{$unified_info{includes}->{$obj}} ],
diff --git a/Configurations/descrip.mms.tmpl b/Configurations/descrip.mms.tmpl
index 2e58b1af9d..416f0ed52e 100644
--- a/Configurations/descrip.mms.tmpl
+++ b/Configurations/descrip.mms.tmpl
@@ -441,12 +441,13 @@ configdata.pm : {- join(" ", sourcefile("Configurations", "descrip.mms.tmpl"), s
   sub generatesrc {
       my %args = @_;
       my $generator = join(" ", @{$args{generator}});
-      my $deps = join(", -\n\t\t", @{$args{deps}});
+      my $generator_incs = join("", map { ' "-I'.$_.'"' } @{$args{generator_incs}});
+      my $deps = join(", -\n\t\t", @{$args{generator_deps}}, @{$args{deps}});
 
       if ($args{src} !~ /\.[sS]$/) {
           return <<"EOF";
 $args{src} : $args{generator}->[0] $deps
-	\$(PERL) $generator > \$@
+	\$(PERL)$generator_incs $generator > \$@
 EOF
       } else {
           die "No method to generate assembler source present.\n";
diff --git a/Configurations/unix-Makefile.tmpl b/Configurations/unix-Makefile.tmpl
index 1676b71b42..900c09fc1d 100644
--- a/Configurations/unix-Makefile.tmpl
+++ b/Configurations/unix-Makefile.tmpl
@@ -808,19 +808,20 @@ configdata.pm: $(SRCDIR)/Configurations/unix-Makefile.tmpl $(SRCDIR)/Configurati
   sub generatesrc {
       my %args = @_;
       my $generator = join(" ", @{$args{generator}});
+      my $generator_incs = join("", map { " -I".$_ } @{$args{generator_incs}});
       my $incs = join("", map { " -I".$_ } @{$args{incs}});
-      my $deps = join(" ", @{$args{deps}});
+      my $deps = join(" ", @{$args{generator_deps}}, @{$args{deps}});
 
       if ($args{src} !~ /\.[sS]$/) {
           return <<"EOF";
 $args{src}: $args{generator}->[0] $deps
-	\$(PERL) $generator > \$@
+	\$(PERL)$generator_incs $generator > \$@
 EOF
       } else {
           if ($args{generator}->[0] =~ /\.pl$/) {
-              $generator = 'CC="$(CC)" $(PERL) '.$generator;
+              $generator = 'CC="$(CC)" $(PERL)'.$generator_incs.' '.$generator;
           } elsif ($args{generator}->[0] =~ /\.m4$/) {
-              $generator = 'm4 -B 8192 '.$generator.' >'
+              $generator = 'm4 -B 8192'.$generator_incs.' '.$generator.' >'
           } elsif ($args{generator}->[0] =~ /\.S$/) {
               $generator = undef;
           } else {
diff --git a/Configurations/windows-makefile.tmpl b/Configurations/windows-makefile.tmpl
index c3233eeb08..159d57c931 100644
--- a/Configurations/windows-makefile.tmpl
+++ b/Configurations/windows-makefile.tmpl
@@ -252,17 +252,18 @@ configdata.pm: {- $config{build_file_template} -} $(SRCDIR)\Configure
       my %args = @_;
       (my $target = $args{src}) =~ s/\.[sS]$/.asm/;
       my $generator = join(" ", @{$args{generator}});
+      my $generator_incs = join("", map { " -I".$_ } @{$args{generator_incs}});
       my $incs = join("", map { " /I ".$_ } @{$args{incs}});
-      my $deps = join(" ", @{$args{deps}});
+      my $deps = join(" ", @{$args{generator_deps}}, @{$args{deps}});
 
       if ($target !~ /\.asm$/) {
           return <<"EOF";
 $target: $args{generator}->[0] $deps
-	\$(PERL) $generator > \$@
+	\$(PERL)$generator_incs $generator > \$@
 EOF
       } else {
           if ($args{generator}->[0] =~ /\.pl$/) {
-              $generator = '$(PERL) '.$generator;
+              $generator = '$(PERL)'.$generator_incs.' '.$generator;
           } elsif ($args{generator}->[0] =~ /\.S$/) {
               $generator = undef;
           } else {
diff --git a/Configure b/Configure
index 4a870c0a82..b32cb942a7 100755
--- a/Configure
+++ b/Configure
@@ -1612,9 +1612,15 @@ EOF
 
         foreach (keys %depends) {
             my $dest = $_;
-            my $ddest = cleanfile($buildd, $_, $blddir);
-            if ($unified_info{rename}->{$ddest}) {
-                $ddest = $unified_info{rename}->{$ddest};
+            my $ddest = cleanfile($sourced, $_, $blddir);
+
+            # If the destination doesn't exist in source, it can only be
+            # a generated file in the build tree.
+            if (! -f $ddest) {
+                $ddest = cleanfile($buildd, $_, $blddir);
+                if ($unified_info{rename}->{$ddest}) {
+                    $ddest = $unified_info{rename}->{$ddest};
+                }
             }
             foreach (@{$depends{$dest}}) {
                 my $d = cleanfile($sourced, $_, $blddir);
@@ -1635,9 +1641,9 @@ EOF
                     $d = $unified_info{rename}->{$d};
                 }
                 $unified_info{depends}->{$ddest}->{$d} = 1;
-                # If we depend on a header file, let's make sure it
-                # can get included
-                if ($d =~ /\.h$/) {
+                # If we depend on a header file or a perl module, let's make
+                # sure it can get included
+                if ($d =~ /\.(h|pm)$/) {
                     my $i = dirname($d);
                     push @{$unified_info{includes}->{$ddest}}, $i
                         unless grep { $_ eq $i } @{$unified_info{includes}->{$ddest}};
@@ -1647,9 +1653,15 @@ EOF
 
         foreach (keys %includes) {
             my $dest = $_;
-            my $ddest = cleanfile($buildd, $_, $blddir);
-            if ($unified_info{rename}->{$ddest}) {
-                $ddest = $unified_info{rename}->{$ddest};
+            my $ddest = cleanfile($sourced, $_, $blddir);
+
+            # If the destination doesn't exist in source, it can only be
+            # a generated file in the build tree.
+            if (! -f $ddest) {
+                $ddest = cleanfile($buildd, $_, $blddir);
+                if ($unified_info{rename}->{$ddest}) {
+                    $ddest = $unified_info{rename}->{$ddest};
+                }
             }
             foreach (@{$includes{$dest}}) {
                 my $i = cleandir($sourced, $_, $blddir);