fix: sync.pl leaves clean working tree (protected files, excludes, no .orig)

dev/import-perl5/config.yaml

@@ -420,8 +420,15 @@ imports:
     type: directory
 
   # Test::Harness - Test harness for running tests (needed by CPAN make test)
+  # Protected because we filter out jar: paths from @INC for child processes
   - source: perl5/cpan/Test-Harness/lib/Test/Harness.pm
     target: src/main/perl/lib/Test/Harness.pm
+    protected: true
+
+  # TAP::Parser::Iterator::Process - Protected because we handle missing fork
+  - source: perl5/cpan/Test-Harness/lib/TAP/Parser/Iterator/Process.pm
+    target: src/main/perl/lib/TAP/Parser/Iterator/Process.pm
+    protected: true
 
   # TAP - Test Anything Protocol modules (required by Test::Harness)
   - source: perl5/cpan/Test-Harness/lib/TAP
@@ -531,8 +538,10 @@ imports:
     target: src/main/perl/lib/Getopt/Std.pm
 
   # Pod::Perldoc - Look up Perl documentation (for jcpan -h)
+  # Protected because we added case-insensitive Pod/ directory search for JAR paths
   - source: perl5/cpan/Pod-Perldoc/lib/Pod/Perldoc.pm
     target: src/main/perl/lib/Pod/Perldoc.pm
+    protected: true
   - source: perl5/cpan/Pod-Perldoc/lib/Pod/Perldoc
     target: src/main/perl/lib/Pod/Perldoc
     type: directory
@@ -688,6 +697,46 @@ imports:
   - source: perl5/pod
     target: src/main/perl/lib/pod
     type: directory
+    exclude:
+      # Build artifacts that shouldn't be copied
+      - .gitignore
+      - Makefile
+      - Makefile.SH
+      - buildtoc
+      - perlmodlib.PL
+      - rofftoc
+      - roffitall
+      - splitman
+      - splitpod
+      # Broken symlinks pointing to ../README.* (don't exist in target)
+      - perlaix.pod
+      - perlamiga.pod
+      - perlandroid.pod
+      - perlbs2000.pod
+      - perlcn.pod
+      - perlcygwin.pod
+      - perlfreebsd.pod
+      - perlhaiku.pod
+      - perlhpux.pod
+      - perlhurd.pod
+      - perlirix.pod
+      - perljp.pod
+      - perlko.pod
+      - perllinux.pod
+      - perlmacosx.pod
+      - perlopenbsd.pod
+      - perlos2.pod
+      - perlos390.pod
+      - perlos400.pod
+      - perlplan9.pod
+      - perlqnx.pod
+      - perlriscos.pod
+      - perlsolaris.pod
+      - perlsynology.pod
+      - perltru64.pod
+      - perltw.pod
+      - perlvos.pod
+      - perlwin32.pod
 
   # Add more imports below as needed
   # Example with minimal fields:

dev/import-perl5/sync.pl

@@ -39,6 +39,14 @@ sub parse_yaml {
             elsif ($line =~ /^\s+protected:\s*(.+)/) {
                 $current_import->{protected} = ($1 =~ /true|yes|1/i) ? 1 : 0;
             }
+            elsif ($line =~ /^\s+exclude:\s*$/) {
+                # Start of exclude list
+                $current_import->{exclude} = [];
+            }
+            elsif ($line =~ /^\s+-\s+(.+)/ && $current_import->{exclude}) {
+                # Exclude list item
+                push @{$current_import->{exclude}}, $1;
+            }
         }
     }
     push @imports, $current_import if $current_import;
@@ -51,7 +59,8 @@ sub parse_yaml {
 sub apply_patch {
     my ($target, $patch_file) = @_;
 
-    my $cmd = "patch -p0 '$target' < '$patch_file'";
+    # --no-backup-if-mismatch prevents creating .orig files
+    my $cmd = "patch --no-backup-if-mismatch -p0 '$target' < '$patch_file'";
     print "  Applying patch: $patch_file\n";
 
     my $result = system($cmd);
@@ -64,7 +73,7 @@ sub apply_patch {
 
 # Copy a directory recursively using rsync
 sub copy_directory {
-    my ($source, $target, $project_root, $protected_files) = @_;
+    my ($source, $target, $project_root, $protected_files, $exclude_patterns) = @_;
 
     # Build rsync command with exclusions for protected files
     my $cmd = "rsync -a";
@@ -88,6 +97,14 @@ sub copy_directory {
         }
     }
 
+    # Add explicit exclude patterns from config
+    if ($exclude_patterns && @$exclude_patterns) {
+        for my $pattern (@$exclude_patterns) {
+            $cmd .= " --exclude='$pattern'";
+            print "  Excluding pattern: $pattern\n";
+        }
+    }
+
     $cmd .= " '$source/' '$target/'";
     print "  Running: $cmd\n";
 
@@ -167,8 +184,8 @@ sub main {
                 };
             }
 
-            # Copy directory using rsync (with protected file exclusions)
-            unless (copy_directory($source, $target, $project_root, \@protected_files)) {
+            # Copy directory using rsync (with protected file exclusions and explicit excludes)
+            unless (copy_directory($source, $target, $project_root, \@protected_files, $import->{exclude})) {
                 $error_count++;
                 next;
             }

src/main/java/org/perlonjava/core/Configuration.java

@@ -33,7 +33,7 @@ public final class Configuration {
      * Automatically populated by Gradle/Maven during build.
      * DO NOT EDIT MANUALLY - this value is replaced at build time.
      */
-    public static final String gitCommitId = "6331b9337";
+    public static final String gitCommitId = "6b6a8bf44";
 
     /**
      * Git commit date of the build (ISO format: YYYY-MM-DD).