common: Fix setting a collection ID on a repository

It was taking a copy of the repository configuration, modifying the
original repository configuration (not the copy), then saving the copy
to disk.

Add a test.

Signed-off-by: Philip Withnall <withnall@endlessm.com>

Closes: #1667
Approved by: mwleeds
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Gitea Version: 1.28.0+dev-477-g8b6ad49a5f