Apply combination logic to merge CLI and persistent configuration #3618
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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 #3541.