Shared directories are not properly cleaned when partitions are enabled
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Issue body
### What needs to get done
- Redesign the state manager to track the partition where files are located
- Redesign the `clean_shared_area()` function to remove the correct files from the list of tracked files from the `StateManager`'s state files
The solution could leverage the data structures added by #664.
### Why it needs to get done
If the same file exists in multiple partitions in a shared directory (`stage` or `prime`), cleaning doesn't work as expected. It will indiscriminately remove the file from all partitions. See [this test](https://github.com/canonical/craft-parts/pull/666/files#diff-0d1cfe4b47f2489eca5633ebe11745aadfdc8e83893f931870ab2399091b70d6R181-R201) for an example.
This is because the `StateManager` does not track files per-partition.
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