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Previously, the GitLab include and ignore lists were only applied during repository enumeration, which meant that they would be ignored after enumeration completed. For large environments, post-enumeration scanning can take days, and it was awkward that the include/ignore lists could effectively not be modified during that time. This PR changes things such that repositories can be configured to be skipped even post-enumeration. Importantly, repositories cannot be "un-ignored" post-enumeration. This is unfortunate, but this PR still represents improvement on the status quo.