GitInput: Include deepClone option in the cache key

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

src/lib/Hydra/Plugin/GitInput.pm

@@ -182,7 +182,7 @@ sub fetchInput {
     # TODO: Fix case where the branch is reset to a previous commit.
     my $cachedInput;
     ($cachedInput) = $self->{db}->resultset('CachedGitInputs')->search(
-        {uri => $uri, branch => $branch, revision => $revision},
+        {uri => $uri, branch => $branch, revision => $revision, isdeepclone => defined($deepClone) ? 1 : 0},
         {rows => 1});
 
     addTempRoot($cachedInput->storepath) if defined $cachedInput;
@@ -223,6 +223,7 @@ sub fetchInput {
                 { uri => $uri
                 , branch => $branch
                 , revision => $revision
+                , isdeepclone => defined($deepClone) ? 1 : 0
                 , sha256hash => $sha256
                 , storepath => $storePath
                 });