refactor!: remove reliance on in-memory file store

Related to https://github.com/renovatebot/renovate/issues/46062, there are some cases where Renovate does in-memory file manipulation, then at some point persists them to disk.

As seen in #44615, this can lead to files needing re-checking.

A refactor (in the next major) to ensure that all file changes are persisted to disk, instead of stored in memory, could reduce this "footgun".