This fixes the following case:
- A-1.0_1 is installed and owns bin/foo.
- A-1.1_1 is in the transaction and depends on B-1.0_1 that owns bin/foo.
- B-1.0_1 is in the transaction and replaces A<1.1_1.
- A-1.1_1 in the transaction now has "skip-obsoletes".
- A is updated to 1.1_1, its metadata file (<pkgname>-files.plist) wasn't removed.
Added two new test cases to verify moving files from/to a dependency.