perf: reduce reference-counting overhead and DBIx::Class warnings

dev/architecture/weaken-destroy.md

@@ -974,6 +974,33 @@ the `classHasDestroy()` check at bless time, which is cached per class. Code
 that actually uses DESTROY classes pays the full tracking cost (increment/
 decrement per reference assignment), but this is by design.
 
+### Tracked-store optimization (2026-07-27)
+
+`RuntimeScalar.setLargeRefCounted()` registered each newly owned reference
+twice in `ScalarRefRegistry`. Once `weaken()` had activated the registry, each
+registration was a synchronized `WeakHashMap.put()`, so tracked stores paid for
+two monitor/map operations even though the second put replaced the same entry.
+
+The optimized path:
+
+- registers the scalar once, after DESTROY-rescue handling;
+- uses the registry without a synchronization wrapper, consistent with
+  PerlOnJava's documented single-threaded runtime model;
+- removes empty reverse weak-reference buckets during `unweaken()`;
+- includes `dev/bench/benchmark_refcount_store.pl` for repeatable measurement.
+
+Median CPU time over three fresh JVM runs of the tracked-store benchmark:
+
+| Revision | CPU time | Change |
+|----------|----------|--------|
+| `master` (`168466619`) | 2.71 s | baseline |
+| optimized branch | 2.41 s | **-11.1%** |
+
+The ordinary method benchmark was unchanged at approximately 2.35 CPU seconds,
+showing no measurable regression before weak-reference bookkeeping is active.
+Correctness validation completed with `make` and the full DBIx::Class suite:
+314 files, 13,121 tests, all successful in 679 wall-clock seconds.
+
 ### Memory Overhead
 
 - **Per-referent:** `refCount` (int, 4 bytes) and `blessId` (int, 4 bytes) on
@@ -983,7 +1010,8 @@ decrement per reference assignment), but this is by design.
   4 bytes), on `RuntimeScalar`. Always present; the JVM may pack the booleans
   into existing object-alignment padding.
 - **WeakRefRegistry:** External identity maps. Only allocated when `weaken()`
-  is called. Zero memory when no weak refs exist.
+  is called. Zero memory when no weak refs exist. Empty per-referent reverse
+  buckets are removed by overwrite, clear, and `unweaken()` paths.
 - **DestroyDispatch caches:** `BitSet` + `ConcurrentHashMap`. Negligible.
 
 ---

dev/bench/README.md

@@ -23,6 +23,7 @@ under PerlOnJava (and optionally system Perl for comparison). Use them to:
 | `benchmark_memory_delta.pl` | Memory growth / leak detection |
 | `benchmark_method.pl` | Method dispatch (class, inheritance) |
 | `benchmark_regex.pl` | Regex compilation and matching |
+| `benchmark_refcount_store.pl` | Tracked reference stores after `weaken()` activates lifecycle bookkeeping |
 | `benchmark_string.pl` | String operations (concat, substr, etc.) |
 
 ## Running

dev/bench/benchmark_refcount_store.pl

@@ -0,0 +1,38 @@
+use strict;
+use warnings;
+use Benchmark;
+use Scalar::Util qw(weaken);
+
+{
+    package RefcountStoreBench;
+
+    sub DESTROY {
+        $main::destroyed++;
+    }
+}
+
+our $destroyed = 0;
+my $object = bless { value => 1 }, 'RefcountStoreBench';
+my $weak = $object;
+weaken($weak);
+
+# Keep enough container slots active to exercise tracked overwrite ownership
+# without measuring allocation of a fresh aggregate on every iteration.
+my @slots = map { $object } 0 .. 1023;
+my $sink = 0;
+
+sub loop_refcount_stores {
+    for my $i (0 .. 999_999) {
+        $slots[$i & 1023] = $object;
+        $sink += $slots[$i & 1023]{value};
+    }
+}
+
+timethis(30, sub {
+    $sink = 0;
+    loop_refcount_stores();
+});
+
+die "tracked object destroyed during benchmark\n"
+    if $destroyed || !defined $weak;
+print "done $sink\n";

dev/modules/dbix_class.md

@@ -543,9 +543,21 @@ can't ship a regression behind that flag.
 
 ---
 
-## Non-Bug Warnings (informational)
+## Environment Warning Fixes (2026-07-27)
+
+- **Generated Exception::Class version mismatches**: Exception::Class 1.45
+  gives generated subclasses version 1.1 while registering
+  `Exception/Class.pm` (version 1.45) as their `%INC` source. The bundled CPAN
+  patch now aligns generated subclass versions with the registered file.
+- **Optional Getopt::Long::Descriptive base classes**: `base::import` still
+  throws the normal catchable "Base class package ... is empty" exception, but
+  no longer prints a duplicate message directly to stderr before throwing.
+- **DynaLoader and bytes version mismatches**: bundled module files now expose
+  the same versions as their Java runtime implementations.
+- Verified `t/00describe_environment.t` has none of these warnings.
+
+## Remaining Non-Bug Warnings (informational)
 
-- **`Mismatch of versions '1.1' and '1.45'`** in `t/00describe_environment.t` for `Params::ValidationCompiler::Exception::Named::Required`: Not a PerlOnJava bug. `Exception::Class` deliberately sets `$INC{$subclass.pm} = __FILE__` on every generated subclass.
 - **`Subroutine is_bool redefined at Cpanel::JSON::XS line 2429`**: Triggered when Cpanel::JSON::XS loads through `@ISA` fallback. Cosmetic only.
 
 ---

dev/modules/moo.md

@@ -16,6 +16,22 @@ All 841/841 Moo subtests now pass across all 71 test files.
 
 ## Completed Fixes
 
+### Readonly Pad Constants Passed Through Constructors — FIXED (2026-07-27)
+
+**2 test files, 6 subtests fixed (tests 17-19 in each accessor-weaken file).**
+
+Root cause: a readonly scalar created by `\ "literal"` is strongly owned by
+the defining subroutine's pad until that subroutine is replaced. Selective
+refcounting cannot see that pad edge. When Moo passed the reference through
+its constructor and weakened the attribute, the constructor temporary reached
+zero and mortal processing cleared the weak reference immediately.
+
+Fix: detect readonly scalars present in the pad constants of currently
+installed named subroutines. Both immediate `weaken()` processing and deferred
+mortal cleanup preserve those references. Replacing the subroutine continues
+to clear them through the existing `clearPadConstantWeakRefs()` optree-reaping
+hook.
+
 ### Category C: Optree Reaping — FIXED (2025-04-09)
 
 **2 test files, 2 subtests fixed (test 19 in each accessor-weaken file).**

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

@@ -126,7 +126,6 @@ public static RuntimeList importBase(RuntimeArray args, int ctx) {
                         // Java bridge stubs for IO::Handle::_sync, or DBIC's
                         // eval-created classes).
                         if (!GlobalVariable.isPackageLoaded(baseClassName)) {
-                            System.err.println("Base class package \"" + baseClassName + "\" is empty.");
                             throw new PerlCompilerException("Base class package \"" + baseClassName + "\" is empty.");
                         }
                     } else {

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

@@ -16,8 +16,6 @@ public static void initialize() {
         DynaLoader dynaLoader = new DynaLoader();
         dynaLoader.initializeExporter();
         dynaLoader.defineExport("EXPORT", "bootstrap");
-        // Set $DynaLoader::VERSION so CPAN dependency checks are satisfied
-        GlobalVariable.getGlobalVariable("DynaLoader::VERSION").set("1.54");
         try {
             dynaLoader.registerMethod("bootstrap", null);
             dynaLoader.registerMethod("boot_DynaLoader", null);
@@ -36,7 +34,8 @@ public static void initialize() {
             dynaLoader.registerMethod("dl_undef_symbols", "dl_empty", null);
             dynaLoader.registerMethod("dl_error", "dl_error", null);
 
-            // Set $DynaLoader::VERSION so CPAN dependency checking works
+            // Match the bundled DynaLoader.pm so runtime and file-based
+            // dependency/version checks report the same value.
             GlobalVariable.getGlobalVariable("DynaLoader::VERSION").set("1.56");
         } catch (NoSuchMethodException e) {
             System.err.println("Warning: Missing DynaLoader method: " + e.getMessage());

src/main/java/org/perlonjava/runtime/runtimetypes/MortalList.java

@@ -985,6 +985,16 @@ private static void processDeferredBase(RuntimeBase base, boolean clearWeakRefsF
                 // generation is wiring Moo metadata. Clearing then makes
                 // nested dispatch call undefer_sub(undef).
                 base.refCount = 1;
+            } else if (base instanceof RuntimeScalarReadOnly
+                    && hasWeakRefs
+                    && RuntimeCode.isInstalledPadConstant(base)) {
+                // A readonly scalar referenced through \("literal") belongs to
+                // its defining subroutine's pad. Constructor/call temporaries
+                // are selectively counted, but that pad ownership is not.
+                // Preserve the weak ref while the sub remains installed;
+                // RuntimeCode.clearPadConstantWeakRefs() clears it when the
+                // sub's glob is replaced, matching Perl optree reaping.
+                base.refCount = 1;
             } else if (base.blessId == 0
                     && hasWeakRefs
                     && (ReachabilityWalker.isReachableFromLiveCodeCaptures(base)

src/main/java/org/perlonjava/runtime/runtimetypes/RuntimeCode.java

@@ -890,6 +890,30 @@ public void clearPadConstantWeakRefs() {
         }
     }
 
+    /**
+     * Return whether a readonly scalar is owned by the optree/pad of a
+     * currently installed named subroutine.
+     *
+     * <p>Pad constants are JVM references that selective refcounting cannot
+     * observe. This targeted lookup lets mortal processing preserve a weak
+     * reference until the owning glob is replaced, when
+     * {@link #clearPadConstantWeakRefs()} performs Perl-compatible optree
+     * reaping.</p>
+     */
+    public static boolean isInstalledPadConstant(RuntimeBase target) {
+        if (target == null) return false;
+        for (RuntimeScalar codeScalar : GlobalVariable.globalCodeRefs.values()) {
+            if (codeScalar == null || !(codeScalar.value instanceof RuntimeCode code)
+                    || code.padConstants == null) {
+                continue;
+            }
+            for (RuntimeBase constant : code.padConstants) {
+                if (constant == target) return true;
+            }
+        }
+        return false;
+    }
+
     /**
      * Release captured variable references. Called when this closure is being
      * discarded (scope exit, undef, or reassignment of the variable holding

src/main/java/org/perlonjava/runtime/runtimetypes/RuntimeScalar.java

@@ -1540,12 +1540,6 @@ private RuntimeScalar setLargeRefCounted(RuntimeScalar value) {
             }
         }
 
-        // Phase B1 (refcount_alignment_52leaks_plan.md): track this
-        // scalar so the reachability walker can enumerate live lexicals.
-        if (newOwned) {
-            ScalarRefRegistry.registerRef(this);
-        }
-
         int preAssignType = this.type;
         Object preAssignValue = this.value;
 
@@ -1597,10 +1591,10 @@ private RuntimeScalar setLargeRefCounted(RuntimeScalar value) {
             newOwned = true;
         }
 
-        // Phase B1 (refcount_alignment_52leaks_plan.md): register this
-        // scalar in ScalarRefRegistry so the reachability walker can
-        // enumerate live ref-holding RuntimeScalars on demand. No-op
-        // when no weaken() has ever been called.
+        // Phase B1 (refcount_alignment_52leaks_plan.md): register this scalar
+        // once, after rescue handling has had a chance to acquire ownership.
+        // This used to run both before and after the assignment, causing two
+        // WeakHashMap.put() calls for every ordinary tracked reference store.
         if (newOwned) {
             ScalarRefRegistry.registerRef(this);
         }

src/main/java/org/perlonjava/runtime/runtimetypes/ScalarRefRegistry.java

@@ -1,10 +1,7 @@
 package org.perlonjava.runtime.runtimetypes;
 
 import java.lang.ref.WeakReference;
-import java.util.Collections;
-import java.util.IdentityHashMap;
 import java.util.Map;
-import java.util.Set;
 import java.util.WeakHashMap;
 
 /**
@@ -31,15 +28,15 @@ public class ScalarRefRegistry {
     // hashCode/equals — RuntimeScalar uses Object's defaults, so this
     // is effectively IdentityHashMap-with-weak-keys.
     private static final Map<RuntimeScalar, Boolean> scalarRegistry =
-            Collections.synchronizedMap(new WeakHashMap<>());
+            new WeakHashMap<>();
 
     // Phase E: optional per-scalar registerRef call-site stacks.
     // Populated only when JPERL_REGISTER_STACKS=1 is set. Uses a
     // WeakHashMap with the same scalar as key, so entries are pruned
     // automatically when the scalar is JVM-GC'd. Lookup via
     // stackFor() is O(1).
     private static final Map<RuntimeScalar, Throwable> registerStacks =
-            Collections.synchronizedMap(new WeakHashMap<>());
+            new WeakHashMap<>();
 
     // Phase B1 performance toggle: when set, skip all registry
     // maintenance. Useful for benchmarks; does NOT affect correctness
@@ -109,9 +106,7 @@ public static Throwable stackFor(RuntimeScalar sc) {
      * unreachable entries first (e.g., freshly-exited lexical scopes).
      */
     public static java.util.List<RuntimeScalar> snapshot() {
-        synchronized (scalarRegistry) {
-            return new java.util.ArrayList<>(scalarRegistry.keySet());
-        }
+        return new java.util.ArrayList<>(scalarRegistry.keySet());
     }
 
     /**
@@ -149,8 +144,6 @@ public static java.util.List<RuntimeScalar> forceGcAndSnapshot() {
      * hold? (Subject to JVM GC between calls.)
      */
     public static int approximateSize() {
-        synchronized (scalarRegistry) {
-            return scalarRegistry.size();
-        }
+        return scalarRegistry.size();
     }
 }

src/main/java/org/perlonjava/runtime/runtimetypes/WeakRefRegistry.java

@@ -146,7 +146,8 @@ public static void weaken(RuntimeScalar ref) {
                         && hasWeakRefsTo(base)
                         && (ReachabilityWalker.isReachableFromRoots(base)
                         || ReachabilityWalker.isReachableFromLiveScalarRegistry(base)
-                        || ReachabilityWalker.isReachableFromLiveCodeCaptures(base))) {
+                        || ReachabilityWalker.isReachableFromLiveCodeCaptures(base)
+                        || RuntimeCode.isInstalledPadConstant(base))) {
                     // A temporary probe can be weakened without owning the last
                     // strong Perl reference. Test::Refcount does this when it
                     // weakens a local copy before calling B::svref_2object().
@@ -170,6 +171,12 @@ && hasWeakRefsTo(base)
             // (new RuntimeScalar(RuntimeScalar)) is mitigated by the fact that such
             // copies don't decrement refCount on cleanup (refCountOwned=false), so
             // they can't cause false-positive refCount==0 destruction.
+        } else if (base.refCount == -1
+                && base instanceof RuntimeScalarReadOnly
+                && RuntimeCode.isInstalledPadConstant(base)) {
+            // The defining subroutine's pad is the strong owner. Its ownership
+            // is not represented in selective refCount, and glob replacement
+            // clears the weak ref explicitly via clearPadConstantWeakRefs().
         } else if (base.refCount == -1 && !(base instanceof RuntimeCode)) {
             // Untracked non-CODE object: transition to WEAKLY_TRACKED so that
             // undefine() and scopeExitCleanup() can clear weak refs
@@ -237,7 +244,10 @@ public static void unweaken(RuntimeScalar ref) {
         if (!weakScalars.remove(ref)) return;
         if (ref.value instanceof RuntimeBase base) {
             Set<RuntimeScalar> weakRefs = referentToWeakRefs.get(base);
-            if (weakRefs != null) weakRefs.remove(ref);
+            if (weakRefs != null) {
+                weakRefs.remove(ref);
+                if (weakRefs.isEmpty()) referentToWeakRefs.remove(base);
+            }
             if (base.refCount >= 0) {
                 base.refCount++;  // restore strong count
                 ref.refCountOwned = true;  // restore ownership

src/main/perl/lib/CPAN/Config.pm

@@ -197,6 +197,8 @@ sub _bootstrap_patches {
           'PerlOnJava/CpanPatches/DBI-1.647/DBI.pm.patch' ],
         [ 'DBI-1.647/PurePerl.pm.patch',
           'PerlOnJava/CpanPatches/DBI-1.647/PurePerl.pm.patch' ],
+        [ 'Exception-Class-1.45/GeneratedSubclassVersion.patch',
+          'PerlOnJava/CpanPatches/Exception-Class-1.45/GeneratedSubclassVersion.patch' ],
         [ 'Net-Server-2.018/Proto.pm.patch',
           'PerlOnJava/CpanPatches/Net-Server-2.018/Proto.pm.patch' ],
         [ 'Device-SerialPort-1.04/NoXsBitsFallback.patch',

src/main/perl/lib/DynaLoader.pm

@@ -13,7 +13,7 @@ package DynaLoader;
 # XSLoader, so DynaLoader's bootstrap() is not needed for normal use.
 #
 
-our $VERSION = '1.54';
+our $VERSION = '1.56';
 
 # Only define bootstrap if not already registered by Java
 BEGIN {

src/main/perl/lib/PerlOnJava/CpanDistroprefs/Exception-Class.yml

@@ -3,12 +3,17 @@ comment: |
   PerlOnJava distroprefs for Exception::Class.
 
   Exception::Class is pure Perl and is needed by Params::ValidationCompiler.
-  Its t/ignore.t suite has one PerlOnJava stack-frame-filter mismatch, but
-  the module otherwise builds and installs.
+  Its t/ignore.t suite has one PerlOnJava stack-frame-filter mismatch. It
+  also assigns generated exception classes version 1.1 while mapping their
+  %INC entries to Exception/Class.pm (version 1.45). This makes consumers
+  such as DBIx::Class report false module/file version mismatches. Keep the
+  generated class version aligned with the file registered in %INC.
 
   Keep the test output visible for signal, but allow CPAN to install it as
   a DateTime prerequisite.
 match:
   distribution: "^DROLSKY/Exception-Class-"
+patches:
+  - "Exception-Class-1.45/GeneratedSubclassVersion.patch"
 test:
   commandline: "PERLONJAVA_TEST_IGNORE_FAILURES"

src/main/perl/lib/PerlOnJava/CpanPatches/Exception-Class-1.45/GeneratedSubclassVersion.patch

@@ -0,0 +1,11 @@
+--- lib/Exception/Class.pm.orig
++++ lib/Exception/Class.pm
+@@ -137,7 +137,7 @@ package $subclass;
+
+ use base qw($isa);
+
+-our \$$version_name = '1.1';
++our \$$version_name = '$VERSION';
+
+ 1;
+

src/main/perl/lib/bytes.pm

@@ -1,5 +1,6 @@
 package bytes;
 
+our $VERSION = '1.08';
 our $hint_bits = 0x00000008;
 
 sub import {