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Search backend: remove query from RepoOptions

Administrator requested to merge cc/remove-repo-options-query into main

Created by: camdencheek

We currently hold a reference to the query in RepoOptions so we can determine whether fork and archived were set explicitly by the user, or whether we used defaults for those values. However, since we only need to know whether they were set explicitly, we can store that instead and reduce the scope of RepoOptions.

Stacked on #34129

Test plan

Checked changed tests and manually verified that excluded repos still show up in the UI as expected.

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