fix(v9): Fix Skills Tracking and Auto-fixable count bugs

BUG #1 - Skills Tracking using ALL issues:
- Skills Tracking was calculating scores using ALL issues (including EXISTING_REST)
- This inflated scores artificially (e.g., Security showing 74/100 instead of 24/100)
- Fixed by filtering to only NEW + EXISTING_MODIFIED issues in category score calculations
- Location: v9-grouped-report-formatter.ts:3494-3514

BUG #2 - Auto-fixable count too low (42/578 instead of 569+):
- Two conflicting canAutoFix() functions existed
- metadata-footer.ts only recognized ~15 hardcoded rules + CheckStyle with "whitespace"
- v9-grouped-report-formatter.ts correctly marked ALL CheckStyle as auto-fixable
- Quick Stats used the restrictive version, Footer used correct count
- Fixed by updating metadata-footer.ts to match correct logic
- Location: metadata-footer.ts:33-48

Impact: Language-agnostic V9 engine fixes benefit all languages (Java, Python, JS, etc.)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: alpsla

packages/agents/src/two-branch/analyzers/v9-grouped-report-formatter.ts

@@ -3491,11 +3491,27 @@ Continue following best practices and consider integrating static analysis into
       const history = await this.skillScoreManager.getScoreTrend(metadata.prAuthorEmail, metadata.repository);
 
       // Calculate current category scores from this PR
-      const security = issues.filter(i => i.detectedCategory === 'Security');
-      const performance = issues.filter(i => i.detectedCategory === 'Performance');
-      const architecture = issues.filter(i => i.detectedCategory === 'Architecture');
-      const dependencies = issues.filter(i => i.detectedCategory === 'Dependencies');
-      const codeQuality = issues.filter(i => i.detectedCategory === 'Code Quality');
+      // BUG FIX: Only count NEW + EXISTING_MODIFIED issues (exclude EXISTING_REST)
+      const security = issues.filter(i =>
+        i.detectedCategory === 'Security' &&
+        (i.category === 'NEW' || i.category === 'EXISTING_MODIFIED')
+      );
+      const performance = issues.filter(i =>
+        i.detectedCategory === 'Performance' &&
+        (i.category === 'NEW' || i.category === 'EXISTING_MODIFIED')
+      );
+      const architecture = issues.filter(i =>
+        i.detectedCategory === 'Architecture' &&
+        (i.category === 'NEW' || i.category === 'EXISTING_MODIFIED')
+      );
+      const dependencies = issues.filter(i =>
+        i.detectedCategory === 'Dependencies' &&
+        (i.category === 'NEW' || i.category === 'EXISTING_MODIFIED')
+      );
+      const codeQuality = issues.filter(i =>
+        i.detectedCategory === 'Code Quality' &&
+        (i.category === 'NEW' || i.category === 'EXISTING_MODIFIED')
+      );
 
       const categoryScores = {
         security: this.calculateCategoryScore(security),

packages/agents/src/two-branch/report/metadata-footer.ts

@@ -28,28 +28,24 @@ export interface IDEFixFile {
 
 /**
  * Check if a group can be auto-fixed by IDE tools
+ * BUG FIX: CheckStyle issues are 100% auto-fixable with IDE formatters
  */
 function canAutoFix(group: IssueGroup | { rule: string; tool: string; severity: string }): boolean {
-  const autoFixableRules = [
-    'SystemPrintln',
+  // CheckStyle issues are 100% auto-fixable with IDE formatters (google-java-format, IntelliJ, etc.)
+  if (group.tool === 'checkstyle') {
+    return true;
+  }
+
+  // PMD rules that support automated fixing
+  const autoFixablePMDRules = [
+    'AvoidUsingVolatile',
     'GuardLogStatement',
-    'LineLength',
-    'WhitespaceAround',
-    'WhitespaceAfter',
-    'AvoidStarImport',
-    'UnusedImports',
-    'RedundantImport',
-    'SimplifyBooleanReturns',
-    'SimplifyBooleanExpressions',
-    'ForLoopCanBeForeach',
-    'UseStringBufferForStringAppends',
-    'ConsecutiveLiteralAppends',
-    'MissingJavadocMethod',
-    'MissingJavadocType'
+    'SystemPrintln',
+    'ClassWithOnlyPrivateConstructorsShouldBeFinal',
+    'ReturnEmptyCollectionRatherThanNull'
   ];
-  
-  return autoFixableRules.includes(group.rule) || 
-         (group.tool === 'checkstyle' && group.rule.toLowerCase().includes('whitespace'));
+
+  return autoFixablePMDRules.includes(group.rule);
 }
 
 /**