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/sql/hydra.sql

@@ -402,9 +402,10 @@ create table CachedGitInputs (
     uri           text not null,
     branch        text not null,
     revision      text not null,
+    isDeepClone   boolean not null,
     sha256hash    text not null,
     storePath     text not null,
-    primary key   (uri, branch, revision)
+    primary key   (uri, branch, revision, isDeepClone)
 );
 
 create table CachedDarcsInputs (