Without this commit, two jobsets using the same repository as input,
but different `deepClone` options, end up incorrectly sharing the same
"checkout" for a given (`uri`, `branch`, `revision`) tuple. The
presence or absence of `.git` is determined by the jobset execution
order.
This patch adds the missing `isDeepClone` boolean to the cache key.
The database upgrade script empties the `CachedGitInputs` table, as we
don't know if existing checkouts are deep clones. Unfortunately, this
generally forces rebuilds even for correct `deepClone` checkouts, as
the binary contents of `.git` are not deterministic.
Fixes#510
