Remove include repos

[jordanTunstill]

Description:

Removed redundant IncludeRepos references from OSS, to match the changes requested in the Enterprise codebase. (https://github.com/trufflesecurity/thog/pull/4996) This is a continuation of #4430, where these changes were part of my original fix. Looking back, the changes here undo the unnecessary work from that PR, while leaving the load-bearing changes that fixed the original issue.

Checklist:

• Tests passing (make test-community)?
• Lint passing (make lint this requires golangci-lint)?

[jordanTunstill]

@sysread @rosecodym Here is the follow up OSS pr i mentioned to remove the interactions with the removed IncludeRepos line.

[shahzadhaider1]

Looks good overall 👍 I just had one question: since include-repos is no longer used in the engine, should we also remove the corresponding CLI flag from main.go? Right now it seems like users could still set the flag, but it wouldn’t have any effect. If there’s a reason for keeping it around (e.g., backward compatibility), then all good, just wanted to double-check.

[jordanTunstill]

@shahzadhaider1 I believe that the gitlab integration uses include-repos as well, and I didn't add include-repos to main.go as part of my initial change. I think, to that end, we should likely keep it around for now. Let me know if you need more info!