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/configuration.md

@@ -95,7 +95,7 @@ listed nor callable.
 
 | Variable | Default | Rules |
 |---|---|---|
-| `READ_ONLY` | `false` | Expose only read-only (GET) operations. `gitea_api_request` stays listed but accepts only GET. |
+| `READ_ONLY` | `false` | Expose only operations annotated read-only (GET plus a few non-mutating POST endpoints such as the render endpoints). `gitea_api_request` stays listed but accepts only GET. |
 | `TOOLSETS` | `all` | Comma separated domains: `admin`, `repo`, `issue`, `pull`, `release`, `wiki`, `org`, `team`, `user`, `actions`, `hook`, `package`, `notification`, `misc`, or `all`. Unknown domains are rejected. `gitea_api_request` belongs to `misc`. |
 | `DISABLED_TOOLS` | empty | Exact tool names to hide, lowercased on load. An unknown name is a startup error that lists the bad names. |