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>

mcp.json

@@ -0,0 +1,11 @@
+{
+  "mcpServers": {
+    "acai-code": {
+      "command": "node",
+      "args": ["mcp-server/stdio.js"],
+      "env": {},
+      "timeout": 30,
+      "startup_timeout": 10
+    }
+  }
+}