🤖 refactor: organize extension docs into dedicated directory

Reorganized extension documentation:
- Created docs/extensions/ directory
- Moved docs/extensions.md → docs/extensions/overview.md
- Moved docs/api/index.md → docs/extensions/api-reference.md
- Removed docs/api/ directory

Updated all references:
- Fixed links in overview.md to point to api-reference.md
- Updated docs/SUMMARY.md with new paths
- Updated typedoc.json to output to docs/extensions/
- Updated package.json and Makefile build scripts

Benefits:
- Cleaner organization (all extension docs in one place)
- Better navigation hierarchy
- Consistent naming (overview.md + api-reference.md)

Generated with cmux

Author: ammar-agent

Makefile

@@ -280,8 +280,8 @@ docs-watch: ## Watch and rebuild documentation
 docs-api: ## Generate extension API reference documentation
 	@echo "$(BLUE)Generating extension API documentation...$(RESET)"
 	@bun x typedoc
-	@mv docs/api/README.md docs/api/index.md 2>/dev/null || true
-	@echo "$(GREEN)✓ API documentation generated in docs/api/index.md$(RESET)"
+	@mv docs/extensions/README.md docs/extensions/api-reference.md 2>/dev/null || true
+	@echo "$(GREEN)✓ API documentation generated in docs/extensions/api-reference.md$(RESET)"
 
 ## Storybook
 storybook: node_modules/.installed ## Start Storybook development server

docs/SUMMARY.md

@@ -20,8 +20,8 @@
 - [Instruction Files](./instruction-files.md)
 - [Project Secrets](./project-secrets.md)
   - [Agentic Git Identity](./agentic-git-identity.md)
-- [Extensions](./extensions.md)
-  - [API Reference](./api/index.md)
+- [Extensions](./extensions/overview.md)
+  - [API Reference](./extensions/api-reference.md)
 
 # Advanced