feat: Implement DeepWiki documentation generation tools

- Added `__init__.py` in `codexlens/tools` for documentation generation.
- Created `deepwiki_generator.py` to handle symbol extraction and markdown generation.
- Introduced `MockMarkdownGenerator` for testing purposes.
- Implemented `DeepWikiGenerator` class for managing documentation generation and file processing.
- Added unit tests for `DeepWikiStore` to ensure proper functionality and error handling.
- Created tests for DeepWiki TypeScript types matching.

.claude/skills/spec-generator/phases/06-5-auto-fix.md

@@ -0,0 +1,144 @@
+# Phase 6.5: Auto-Fix
+
+Automatically repair specification issues identified in Phase 6 Readiness Check.
+
+## Objective
+
+- Parse readiness-report.md to extract Error and Warning items
+- Group issues by originating Phase (2-5)
+- Re-generate affected sections with error context injected into CLI prompts
+- Re-run Phase 6 validation after fixes
+
+## Input
+
+- Dependency: `{workDir}/readiness-report.md` (Phase 6 output)
+- Config: `{workDir}/spec-config.json` (with iteration_count)
+- All Phase 2-5 outputs
+
+## Execution Steps
+
+### Step 1: Parse Readiness Report
+
+```javascript
+const readinessReport = Read(`${workDir}/readiness-report.md`);
+const specConfig = JSON.parse(Read(`${workDir}/spec-config.json`));
+
+// Load glossary for terminology consistency during fixes
+let glossary = null;
+try {
+  glossary = JSON.parse(Read(`${workDir}/glossary.json`));
+} catch (e) { /* proceed without */ }
+
+// Extract issues from readiness report
+// Parse Error and Warning severity items
+// Group by originating phase:
+//   Phase 2 issues: vision, problem statement, scope, personas
+//   Phase 3 issues: requirements, acceptance criteria, priority, traceability
+//   Phase 4 issues: architecture, ADRs, tech stack, data model, state machine
+//   Phase 5 issues: epics, stories, dependencies, MVP scope
+
+const issuesByPhase = {
+  2: [], // product brief issues
+  3: [], // requirements issues
+  4: [], // architecture issues
+  5: []  // epics issues
+};
+
+// Parse structured issues from report
+// Each issue: { severity: "Error"|"Warning", description: "...", location: "file:section" }
+
+// Map phase numbers to output files
+const phaseOutputFile = {
+  2: 'product-brief.md',
+  3: 'requirements/_index.md',
+  4: 'architecture/_index.md',
+  5: 'epics/_index.md'
+};
+```
+
+### Step 2: Fix Affected Phases (Sequential)
+
+For each phase with issues (in order 2 -> 3 -> 4 -> 5):
+
+```javascript
+for (const [phase, issues] of Object.entries(issuesByPhase)) {
+  if (issues.length === 0) continue;
+
+  const errorContext = issues.map(i => `[${i.severity}] ${i.description} (at ${i.location})`).join('\n');
+
+  // Read current phase output
+  const currentOutput = Read(`${workDir}/${phaseOutputFile[phase]}`);
+
+  Bash({
+    command: `ccw cli -p "PURPOSE: Fix specification issues identified in readiness check for Phase ${phase}.
+Success: All listed issues resolved while maintaining consistency with other documents.
+
+CURRENT DOCUMENT:
+${currentOutput.slice(0, 5000)}
+
+ISSUES TO FIX:
+${errorContext}
+
+${glossary ? `GLOSSARY (maintain consistency):
+${JSON.stringify(glossary.terms, null, 2)}` : ''}
+
+TASK:
+- Address each listed issue specifically
+- Maintain all existing content that is not flagged
+- Ensure terminology consistency with glossary
+- Preserve YAML frontmatter and cross-references
+- Use RFC 2119 keywords for behavioral requirements
+- Increment document version number
+
+MODE: analysis
+EXPECTED: Corrected document content addressing all listed issues
+CONSTRAINTS: Minimal changes - only fix flagged issues, do not restructure unflagged sections
+" --tool gemini --mode analysis`,
+    run_in_background: true
+  });
+
+  // Wait for result, apply fixes to document
+  // Update document version in frontmatter
+}
+```
+
+### Step 3: Update State
+
+```javascript
+specConfig.phasesCompleted.push({
+  phase: 6.5,
+  name: "auto-fix",
+  iteration: specConfig.iteration_count,
+  phases_fixed: Object.keys(issuesByPhase).filter(p => issuesByPhase[p].length > 0),
+  completed_at: new Date().toISOString()
+});
+Write(`${workDir}/spec-config.json`, JSON.stringify(specConfig, null, 2));
+```
+
+### Step 4: Re-run Phase 6 Validation
+
+```javascript
+// Re-execute Phase 6: Readiness Check
+// This creates a new readiness-report.md
+// If still Fail and iteration_count < 2: loop back to Step 1
+// If Pass or iteration_count >= 2: proceed to handoff
+```
+
+## Output
+
+- **Updated**: Phase 2-5 documents (only affected ones)
+- **Updated**: `spec-config.json` (iteration tracking)
+- **Triggers**: Phase 6 re-validation
+
+## Quality Checklist
+
+- [ ] All Error-severity issues addressed
+- [ ] Warning-severity issues attempted (best effort)
+- [ ] Document versions incremented for modified files
+- [ ] Terminology consistency maintained
+- [ ] Cross-references still valid after fixes
+- [ ] Iteration count not exceeded (max 2)
+
+## Next Phase
+
+Re-run [Phase 6: Readiness Check](06-readiness-check.md) to validate fixes.