docs: fix the claude mcp add form, pin the package index, document known limitations

The --env option swallowed the server name, so the stdio command is reordered. uvx now always
names the project registry because the package name is not registered on public PyPI.
README gains a Known limitations section, the READ_ONLY wording is corrected, packaging.md
warns about --extra-index-url and the Le Chat admin requirement is mentioned.

docs/troubleshooting.md

@@ -22,8 +22,10 @@ Gitea's sanitized message, and the audit log has one event per call (see
 
 stdout carries only JSON-RPC. If a wrapper script prints to stdout before the server starts, the
 client fails to parse the stream. Logs go to stderr; look at the client's MCP server log.
-`uvx` needs access to the package index that hosts `aegis-gitea-mcp`, see
-[packaging.md](packaging.md).
+`uvx` needs access to the package index that hosts `aegis-gitea-mcp`: pass
+`--index https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/`, see
+[packaging.md](packaging.md). If you register the server with `claude mcp add`, put `--env`
+before `--transport stdio` and the server name, as `setup` prints it.
 
 ## Tool calls fail