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fix(internal/gapicgen): don't regen files that have been deleted (#3471)
Currently this method will find all the files that haven been updated since the last hash. This is then used to find out which packages will need to be regenerated. We should not try to regenerate files that have been deleted, this causes a file does not exist error when running the generator. The provided flag restricts to files that: - (A) Added - (C) Copied - (M) Modified - (R) Renamed
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