fix: detect __DATA__/__END__ and no Module; terminators in source filters

dev/design/source_filters.md

@@ -475,6 +475,37 @@ print "X";  # Should print Y
 ### Remaining Work
 - [ ] **Phase 4**: Add method filter support (currently returns original source for method filters)
 - [ ] Add debug environment variable documentation (JPERL_FILTER_DEBUG=1)
+- [ ] **Phase 5**: Fix FILTER_ONLY @transforms issue in Java instead of patching Filter::Simple (see below)
+
+### Known Issues
+
+#### FILTER_ONLY @transforms Scope Issue (2026-03-27)
+
+**Problem**: When multiple filter modules using `FILTER_ONLY` are loaded in sequence, the second filter's `$multitransform` closure incorrectly includes transforms from the first module.
+
+**Root Cause**: In Filter::Simple, `@transforms` is a package variable. In native Perl, this works because filters process source incrementally - each filter completes before the next filter module is loaded. In PerlOnJava, we tokenize upfront then apply filters, so multiple filter modules may be loaded before any filter runs, causing `@transforms` to accumulate transforms from different modules.
+
+**Current Fix**: Patched `Filter::Simple.pm` to make `@transforms` lexical in `FILTER_ONLY`:
+```perl
+sub FILTER_ONLY {
+    my $caller = caller;
+    my @transforms;  # Made lexical instead of package-scoped
+    ...
+}
+```
+
+**TODO - Proper Java-side Fix**: The ideal solution would be to fix this in PerlOnJava's module loading code:
+1. Before loading a module that may use `FILTER_ONLY`, save `@Filter::Simple::transforms`
+2. Clear `@Filter::Simple::transforms` 
+3. After module loading completes, restore the saved value
+
+This would allow using unmodified upstream Filter::Simple. The challenge is detecting which modules will use `FILTER_ONLY` before loading them. Possible approaches:
+- Clear `@Filter::Simple::transforms` before every `require` (may have side effects)
+- Track filter module loading depth and isolate transforms per level
+- Hook into Filter::Simple's FILTER_ONLY to auto-reset before each call
+
+**Files affected by current fix**:
+- `src/main/perl/lib/Filter/Simple.pm` (marked as `protected: true` in config.yaml)
 
 ### Files Modified
 - `src/main/java/org/perlonjava/runtime/perlmodule/FilterUtilCall.java`

dev/import-perl5/config.yaml

@@ -640,6 +640,17 @@ imports:
   - source: perl5/cpan/Term-ANSIColor/lib/Term/ANSIColor.pm
     target: src/main/perl/lib/Term/ANSIColor.pm
 
+  # Filter::Simple - Simplified source filtering (used by Log::Log4perl :resurrect, etc.)
+  # Protected: has PerlOnJava-specific fix for @transforms scope in FILTER_ONLY
+  - source: perl5/dist/Filter-Simple/lib/Filter/Simple.pm
+    target: src/main/perl/lib/Filter/Simple.pm
+    protected: true
+
+  # Tests for Filter::Simple
+  - source: perl5/dist/Filter-Simple/t
+    target: perl5_t/Filter-Simple
+    type: directory
+
   # Class::Struct - Declare struct-like datatypes as Perl classes
   # Required by File::stat.pm
   - source: perl5/lib/Class/Struct.pm

docs/about/changelog.md

@@ -31,6 +31,8 @@ Release history of PerlOnJava. See [Roadmap](roadmap.md) for future plans.
   - The interpreter mode excels at dynamic eval STRING operations (46x faster than compilation for unique strings, matching Perl 5 performance). For general code, it runs only 15% slower than Perl 5. It is also useful for implementing debugging, handling "Method too large" errors, and enabling Android and GraalVM compatibility.
 - Planned release date: 2026-04-10.
 
+- Add modules: `Filter::Simple` with `FILTER` and `FILTER_ONLY` support.
+
 - Work in Progress
   - PerlIO
     - `get_layers`
@@ -45,7 +47,6 @@ Release history of PerlOnJava. See [Roadmap](roadmap.md) for future plans.
     - `ungetc`
     - Auto-bless filehandle into IO::Handle subclass
   - IO::Seekable
-  - Filter::Simple
   - Math::BigInt
   - Text::ParseWords
   - Text::Tabs

docs/reference/feature-matrix.md

@@ -692,6 +692,7 @@ The `:encoding()` layer supports all encodings provided by Java's `Charset.forNa
 - ✅  **ExtUtils::MakeMaker** module: PerlOnJava version installs pure Perl modules directly.
 - ✅  **Fcntl** module
 - ✅  **FileHandle** module
+- ✅  **Filter::Simple** module: `FILTER` and `FILTER_ONLY` for source code filtering.
 - ✅  **File::Basename** use the same version as Perl.
 - ✅  **File::Find** use the same version as Perl.
 - ✅  **File::Spec::Functions** module.

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 = "8bb1eff41";
+    public static final String gitCommitId = "9153c9ba8";
 
     /**
      * Git commit date of the build (ISO format: YYYY-MM-DD).

src/main/java/org/perlonjava/frontend/parser/Whitespace.java

@@ -51,12 +51,12 @@ public static int skipWhitespace(Parser parser, int tokenIndex, List<LexerToken>
                         if (tokenIndex + 1 < tokens.size() && tokens.get(tokenIndex + 1).type == LexerTokenType.IDENTIFIER) {
                             boolean inPod = true;
 
-                            // Skip through pod section until 'cut' or 'end' is found
+                            // Skip through pod section until '=cut' is found
+                            // Note: '=end formatname' only ends a =begin block, not the entire POD section
                             while (tokenIndex < tokens.size() && inPod) {
                                 String podEqual = tokens.get(tokenIndex).text;
                                 String podToken = tokens.get(tokenIndex + 1).text;
-                                if (podEqual.equals("=")
-                                        && (podToken.equals("cut") || podToken.equals("end"))) {
+                                if (podEqual.equals("=") && podToken.equals("cut")) {
                                     inPod = false; // End of pod
                                 }
 

src/main/java/org/perlonjava/runtime/perlmodule/FilterUtilCall.java

@@ -293,6 +293,29 @@ public static String applyFilters(String sourceCode) {
                             if (debug) {
                                 System.err.println("[FILTER] Got chunk: " + chunk);
                             }
+
+                            // Check if the chunk ends with __DATA__, __END__, or "no Module;" terminator
+                            // If so, stop filtering and append remaining source unchanged
+                            // This is important for Filter::Simple which stops at these terminators
+                            // Pattern matches:
+                            // - __DATA__ or __END__ at end of line
+                            // - "no ModuleName;" at start of line (with optional comment)
+                            if (chunk.matches("(?sm).*^__(?:DATA|END)__\\s*$") ||
+                                chunk.matches("(?sm).*^\\s*no\\s+[\\w:]+\\s*;.*$")) {
+                                // Append remaining source unchanged
+                                if (debug) {
+                                    System.err.println("[FILTER] Hit terminator, currentLine=" + context.currentLine + 
+                                        ", totalLines=" + context.sourceLines.length);
+                                }
+                                while (context.currentLine < context.sourceLines.length) {
+                                    filteredCode.append(context.sourceLines[context.currentLine]);
+                                    context.currentLine++;
+                                }
+                                continueFiltering = false;
+                                if (debug) {
+                                    System.err.println("[FILTER] Hit __DATA__/__END__ terminator, appending remaining source unchanged");
+                                }
+                            }
                         }
 
                         // Check status - convert to scalar if it's a list
@@ -318,7 +341,8 @@ public static String applyFilters(String sourceCode) {
             }
 
             if (debug) {
-                System.err.println("[FILTER] Final filtered code: " + filteredCode.toString().substring(0, Math.min(200, filteredCode.length())));
+                System.err.println("[FILTER] Final filtered code length: " + filteredCode.length());
+                System.err.println("[FILTER] Final filtered code: " + filteredCode.toString());
             }
             return filteredCode.toString();
 

src/main/perl/lib/Filter/Simple.pm

@@ -144,6 +144,13 @@ sub FILTER (&;$) {
 
 sub FILTER_ONLY {
     my $caller = caller;
+    # PerlOnJava fix: @transforms must be lexical, not package-scoped.
+    # In native Perl, filters process source incrementally during parsing,
+    # so each filter completes before the next filter module is loaded.
+    # In PerlOnJava, we tokenize upfront then apply filters, so multiple
+    # filter modules may be loaded before any filter runs. Using a package
+    # variable causes transforms from different modules to accumulate.
+    my @transforms;
     while (@_ > 1) {
         my ($what, $how) = splice(@_, 0, 2);
         fail "Unknown selector: $what"

src/test/resources/unit/pod.t

@@ -0,0 +1,77 @@
+# Test POD (Plain Old Documentation) parsing
+
+use strict;
+use warnings;
+
+print "1..6\n";
+
+my $test = 1;
+
+=pod
+
+Basic POD block
+
+=cut
+
+print "ok $test - basic POD block\n";
+$test++;
+
+=head1 NAME
+
+Test documentation
+
+=cut
+
+print "ok $test - =head1 POD block\n";
+$test++;
+
+=begin scrumbly
+
+This is inside a scrumbly format block.
+
+=end scrumbly
+
+This text is between =end scrumbly and =cut.
+Per perlpod, this should be treated as POD, not code.
+foo bar baz
+
+=cut
+
+print "ok $test - =begin/=end block with trailing content\n";
+$test++;
+
+=begin comment
+
+A comment block
+
+=end comment
+
+More POD content after =end but before =cut
+
+=cut
+
+print "ok $test - =begin comment block\n";
+$test++;
+
+=pod
+
+=end
+
+standalone =end stays in POD
+
+=cut
+
+print "ok $test - standalone =end inside POD\n";
+$test++;
+
+=begin cut
+
+this format is named 'cut'
+
+=end cut
+
+still in POD after =end cut
+
+=cut
+
+print "ok $test - =begin cut / =end cut format\n";