@@ -120,6 +120,7 @@ amplihack copilot
120120- [ Profile Management] ( PROFILE_MANAGEMENT.md ) - Multiple environment configurations
121121- [ Proxy Configuration] ( PROXY_CONFIG_GUIDE.md ) - Network proxy setup (Azure OpenAI, custom endpoints)
122122- [ Hook Configuration] ( HOOK_CONFIGURATION_GUIDE.md ) - Customize framework behavior
123+ - [ Configure Hook Timeouts] ( howto/configure-hook-timeouts.md ) - Adjust timeout thresholds for stop hook operations
123124- [ Memory Configuration Consent] ( features/memory-consent-prompt.md ) - Intelligent memory settings with timeout protection
124125- [ Verify .claude/ Staging] ( howto/verify-claude-staging.md ) - Check that framework files are properly staged
125126
@@ -147,6 +148,7 @@ Understand the philosophy and architecture behind amplihack.
147148- [ Project Overview] ( claude/context/PROJECT.md ) - System architecture
148149- [ Development Patterns] ( claude/context/PATTERNS.md ) - Proven implementation patterns
149150- [ Unified Staging Architecture] ( concepts/unified-staging-architecture.md ) - How .claude/ staging works across all commands
151+ - [ Hook Timeout Tracking] ( concepts/hook-timeout-tracking.md ) - How stop hook manages 30s timeout budget
150152- [ Blarify Architecture] ( blarify_architecture.md ) - Understanding the Blarify integration
151153- [ Documentation Knowledge Graph] ( documentation_knowledge_graph.md ) - How docs connect
152154
@@ -425,8 +427,8 @@ Robust handling of conversation compaction in long sessions:
425427
426428- [ Smart Memory Management] ( features/smart-memory-management.md ) - Automatic Node.js memory optimization for Claude Code
427429- [ Claude.md Preservation] ( features/claude-md-preservation.md ) - Preserve custom instructions
428- <!-- Neo4j removed - now using Kuzu embedded database (no session cleanup needed) -->
429- <!-- - [Shutdown Detection](concepts/shutdown-detection.md) - Graceful exit handling (see stop-hook-exit-hang in Troubleshooting) -->
430+ <!-- Neo4j removed - now using Kuzu embedded database (no session cleanup needed) -->
431+ <!-- - [Shutdown Detection](concepts/shutdown-detection.md) - Graceful exit handling (see stop-hook-exit-hang in Troubleshooting) -->
430432
431433### Third-Party Integrations
432434
@@ -555,6 +557,7 @@ Quick references, guides, and additional resources.
555557### Quick References
556558
557559- [ Command Selection Guide] ( commands/COMMAND_SELECTION_GUIDE.md ) - Choose the right command
560+ - [ Hook Timeout API Reference] ( reference/hook-timeout-api.md ) - TimeoutTracker implementation details
558561- [ Platform Bridge API Reference] ( reference/platform-bridge-api.md ) - Complete API documentation
559562- [ Doc Graph Quick Reference] ( doc_graph_quick_reference.md ) - Navigate documentation
560563<!-- Neo4j Quick Reference removed - now using Kuzu embedded database -->
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