Add .gitignore, remove __pycache__ from tracking, and update MCP/orchestrator modules

- Add .gitignore to exclude .env, __pycache__, node_modules, and IDE files
- Remove all __pycache__ bytecode files from version control
- Add MCP config files (mcp.json, mcp.json.example)
- Add MCP manager, registry, and config modules
- Update routes, orchestrator engine, and agent base with latest changes

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

.gitignore

@@ -0,0 +1,28 @@
+# Environment variables
+.env
+.env.local
+.env.*.local
+
+# Python
+__pycache__/
+*.pyc
+*.pyo
+*.egg-info/
+dist/
+build/
+.venv/
+venv/
+
+# Node
+node_modules/
+npm-debug.log*
+
+# OS
+.DS_Store
+Thumbs.db
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo