Revert "fix: Increase stop hook timeout from 30s to 2 minutes"

This reverts commit d94cae0.

Author: Ubuntu

.claude/settings.json

@@ -49,7 +49,7 @@
           {
             "type": "command",
             "command": ".claude/tools/amplihack/hooks/stop.py",
-            "timeout": 120000
+            "timeout": 30000
           }
         ]
       }

docs/index.md

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

src/amplihack/utils/uvx_settings_template.json

@@ -46,7 +46,7 @@
           {
             "type": "command",
             "command": ".claude/tools/amplihack/hooks/stop.py",
-            "timeout": 120000
+            "timeout": 30000
           }
         ]
       }
@@ -72,17 +72,6 @@
           }
         ]
       }
-    ],
-    "SessionEnd": [
-      {
-        "hooks": [
-          {
-            "type": "command",
-            "command": ".claude/tools/amplihack/hooks/session_end.py",
-            "timeout": 10000
-          }
-        ]
-      }
     ]
   }
 }