Fix docs-mcp cache directory ownership checks

docs/troubleshooting.md

@@ -40,3 +40,34 @@ section. Keep default sources small, and add profiles only when you need them.
 
 Cloudflare and other large docs sets can take significantly longer than the
 default source profile.
+
+## Docs Tools Say Index Manager Not Initialized
+
+If `docs_query` or `docs_refresh` returns `Index manager not initialized` while
+`/status` still responds, the HTTP wrapper is up but `llms-txt-mcp` failed to
+initialize its embedding model or Chroma database. Check the container logs:
+
+```sh
+docker logs context-kit-docs-mcp
+```
+
+A common cause is Docker creating the bind-mounted cache directories as `root`
+before Context Kit created them as the host user. Look for errors like:
+
+```text
+Permission denied: '/models/models--BAAI--bge-small-en-v1.5'
+unable to open database file
+```
+
+Fix ownership and restart:
+
+```sh
+DATA_DIR="${CONTEXT_KIT_DATA_DIR:-$HOME/.local/share/context-kit}"
+sudo chown -R "$(id -u):$(id -g)" "$DATA_DIR/docs" "$DATA_DIR/models"
+bin/context-kit restart
+```
+
+`bin/context-kit start` now pre-creates these directories and `doctor` reports
+existing directories that are not writable by the current user. If an assistant
+client reports `Session not found` after restarting `docs-mcp`, restart the
+assistant so it opens a fresh Streamable HTTP MCP session.