Apply combination logic to merge CLI and persistent configuration (#3618)
## Summary
If you have (e.g.) `extra-index-url` in your configuration file _and_
provide `--extra-index-url` on the command-line, we now merge the
options rather than ignoring those in the configuration file. As such,
merging the CLI and the persistent configuration is now semantically
identical to how we merge (project persistent configuration) with (user
persistent configuration).
Closes https://github.com/astral-sh/uv/issues/3541.