1020460 - Fixed removing skip list from an existing repository

There are a few things going on in here:

= repo_create_update =
The convert_removed_options call was removed from _pre_config. This is called earlier in the flow. This was actually really bad; I'm surprised we didn't see more bugs about it.

= repo_options =
The parsing logic for the skip list correctly handles an empty string, which is the convention for removing a configuration value.

= test_extensions_repo_create_update =
The bulk of this was swapping two tests. There was a create test in the update suite and vice-versa. Github is trying to compare them as a diff so it's hard to tell that's what happened.

A new test was added for verifying `--skip ""` is correctly translated in the submitted configuration.