Deprectate buggy/incorrect Rls/PkgFile::IsOk methods

With the advent of compressed files and especially with in-memory
post-processed files the simple assumptions made in IsOk are no longer
true. Worse, they are at best duplicates of checks performed by the
cache generation (and validation) earlier and isn't used in too many
places. It is hence best to simply get right of these calls instead of
trying to fix them.

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