Don't fail when trying to prune pack which is already gone

Update the TestRepository.prunePacked so that it doesn't fail if a pack
to be pruned is already gone.
It is especially handy when the prunePacked function is called in
`TestRepository.packAndPrune` function after the repo moves on after
GC was performed.

Change-Id: I01b4ddbaddec1fdc24cfbb967e0edfe0de6c4b7c