Cachi2 prefetching is making changes on a source

[eskultety]

We only use a working copy of the input source repository for the Yarn backends. All other package manager backends work on top of the input source directly which may result in some operations we perform dirtying the repo which is completely undesirable.
Unlike #707 the global fix isn't as straight forward since the main issue only pops up with integration tests which also compare the contents of our .build-config.json file where we fill out incorrect path data for all project_files, using the temporary working copy path instead of the actual input repo.

We need to make sure that while all operations are performed on top of the working copy, any generated build-config data are tied to the original input repo path as the temporary working copy is discarded by the time both .build-config.json and SBOM are dumped to the disk.

Extends: #707