🤖 refactor: use TypeDoc HTML instead of markdown for API reference

- Remove typedoc-plugin-markdown dependency
- Generate HTML to docs/api/ instead of markdown
- Update links in overview.md to point to TypeDoc HTML
- Remove api-reference.md from SUMMARY.md
- Simpler build process (no markdown conversion)
- Better UX: TypeDoc HTML has search, navigation tree, type links
- Reduces complexity and maintenance burden

Benefits:
- Professional API documentation with built-in features
- No need for Shiki preprocessing of API docs
- Separate concerns: user guides (mdBook) vs API reference (TypeDoc)
- Standard pattern used by most TypeScript libraries

Author: ammar-agent

.gitignore

@@ -118,3 +118,4 @@ docs/theme/pagetoc.css
 docs/theme/pagetoc.js
 # Generated documentation theme assets
 docs/theme/code-blocks.css
+docs/api/

Makefile

@@ -277,11 +277,10 @@ docs-build: docs-api ## Build documentation (with Shiki preprocessor)
 docs-watch: ## Watch and rebuild documentation
 	@cd docs && mdbook watch
 
-docs-api: ## Generate extension API reference documentation
+docs-api: ## Generate extension API reference documentation (HTML)
 	@echo "$(BLUE)Generating extension API documentation...$(RESET)"
 	@bun x typedoc
-	@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)"
+	@echo "$(GREEN)✓ API documentation generated in docs/api/$(RESET)"
 
 ## Storybook
 storybook: node_modules/.installed ## Start Storybook development server

docs/SUMMARY.md

@@ -21,7 +21,6 @@
 - [Project Secrets](./project-secrets.md)
   - [Agentic Git Identity](./agentic-git-identity.md)
 - [Extensions](./extensions/overview.md)
-  - [API Reference](./extensions/api-reference.md)
 
 # Advanced