* Fix worktree scan by setting EnableDotGitCommonDir
* Change `PlainOpenOptions` to set `EnableDotGitCommonDir` to true.
In every current usage of this function, it is on an already-cloned
repository, so it should always be valid to have this set. By doing
so, it should fix some issues with worktrees.
* Remove unused go.mod replace directives
* Remove replace directives for libraries that are not in use.
* Refactor Engine to wait for workers in a Finish method
This should allow the engine to run multiple concurrent scans if
desired before shutting down.
Additionally, this commit refactors some of the printing logic to the
output package.
* Fix tests
