fix: self-clobber when updating/downgrading packages

[wolfv]

This fixes an issue where if you install zlib=1.2 and then update to zlib=1.3 all files were detected as "clobbered".

This made changes really slow (e.g. when changing the version of Rust) because the un-clobbering is not really an optimized function and is expected to run only for a few files.