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 prunePacked
function is called in `TestRepository.packAndPrune` function after repo
moves on after the GC was performed.

Change-Id: I01b4ddbaddec1fdc24cfbb967e0edfe0de6c4b7c