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/packaging.md

@@ -44,28 +44,46 @@ Dependencies are pinned in `uv.lock`; `uv sync` reproduces the environment.
 
 ## Install from the Gitea registry
 
+Index URL: `https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/`
+
 Stable:
 
 ```bash
-uv pip install \
-  --extra-index-url https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/ \
-  aegis-gitea-mcp
-
-# or run it without installing into an environment:
+# run it without installing into an environment (recommended):
 uvx --index https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/ aegis-gitea-mcp
+
+# or install it into an environment:
+uv pip install --index https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/ aegis-gitea-mcp
 ```
 
-Dev (newest pre-release build):
+Dev (newest pre-release build, package `aegis-gitea-mcp-dev`):
 
 ```bash
-uv pip install --pre \
-  --extra-index-url https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/ \
-  aegis-gitea-mcp-dev
+uvx --index https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/ --prerelease allow aegis-gitea-mcp-dev
 ```
 
-The registry holds only this project's packages and does not proxy PyPI, so it is added as an
-extra index and the dependencies (`mcp`, `httpx`, ...) still come from PyPI. With `pip` use
-`--extra-index-url` the same way.
+The registry holds only this project's packages and does not proxy PyPI, so it is added with
+`--index` and the dependencies (`mcp`, `httpx`, ...) still come from PyPI. uv's default index
+strategy (`first-index`) takes a package from the first index that has it and never mixes
+versions across indexes, so with `--index` the name `aegis-gitea-mcp` is always taken from
+this registry, even if somebody registers it on PyPI.
+
+Do not use `--extra-index-url` with `pip`. It merges the indexes, and `pip` picks the highest
+version from either: whoever publishes `aegis-gitea-mcp` on PyPI with a higher version number
+wins (dependency confusion), and the package would run with your Gitea token in its
+environment. With `pip`, fetch the wheel from this registry alone, then install it:
+
+```bash
+pip download --no-deps --index-url https://git.hiddenden.cafe/api/packages/Hiddenden/pypi/simple/ aegis-gitea-mcp -d wheels/
+pip install wheels/aegis_gitea_mcp-*.whl
+```
+
+The name is not registered on public PyPI. Publishing there is intentionally not configured, but
+the owner should reserve both names (`aegis-gitea-mcp`, `aegis-gitea-mcp-dev`) on PyPI so nobody
+else can take them. Until then every install command above must name the index.
+
+To run from a clone instead of a registry:
+`uv run --directory /path/to/AegisGitea-MCP aegis-gitea-mcp serve`.
 
 ## Publishing