Exa MCP servers were always filtered out because the native Exa integration covers web_search_exa. But configs that explicitly request web_fetch_exa or web_search_advanced_exa have no native equivalent, so filtering them made /mcp reconnect exa fail and hid those tools. Keep the MCP server mounted when its tools restriction includes anything beyond web_search_exa, while still extracting the API key for native search.
- Moved documentation files from packages/coding-agent/docs/ to root docs/ directory to flatten the documentation structure.
- Updated all internal documentation links to account for the new file locations, adjusting relative paths to maintain correct references across the monorepo.
- Updated README.md and issue template configuration to reference documentation at the new root docs/ location instead of packages/coding-agent/docs/.