packfile: refactor `find_pack_entry()` to work on the packfile store
The function `find_pack_entry()` doesn't work on a specific packfile
store, but instead works on the whole repository. This causes a bit of a
conceptual mismatch in its callers:
- `packfile_store_freshen_object()` supposedly acts on a store, and
its callers know to iterate through all sources already.