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Apply combination logic to merge CLI and persistent configuration (as…
…tral-sh#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 astral-sh#3541.
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