diff --git a/src/lib/Hydra/Plugin/GitInput.pm b/src/lib/Hydra/Plugin/GitInput.pm
index 3fbf50f0..848c0dee 100644
--- a/src/lib/Hydra/Plugin/GitInput.pm
+++ b/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
                 });
diff --git a/src/lib/Hydra/Schema/CachedGitInputs.pm b/src/lib/Hydra/Schema/CachedGitInputs.pm
index d85f4970..4a2b102b 100644
--- a/src/lib/Hydra/Schema/CachedGitInputs.pm
+++ b/src/lib/Hydra/Schema/CachedGitInputs.pm
@@ -50,6 +50,11 @@ __PACKAGE__->table("cachedgitinputs");
   data_type: 'text'
   is_nullable: 0
 
+=head2 isdeepclone
+
+  data_type: 'boolean'
+  is_nullable: 0
+
 =head2 sha256hash
 
   data_type: 'text'
@@ -69,6 +74,8 @@ __PACKAGE__->add_columns(
   { data_type => "text", is_nullable => 0 },
   "revision",
   { data_type => "text", is_nullable => 0 },
+  "isdeepclone",
+  { data_type => "boolean", is_nullable => 0 },
   "sha256hash",
   { data_type => "text", is_nullable => 0 },
   "storepath",
@@ -85,14 +92,16 @@ __PACKAGE__->add_columns(
 
 =item * L</revision>
 
+=item * L</isdeepclone>
+
 =back
 
 =cut
 
-__PACKAGE__->set_primary_key("uri", "branch", "revision");
+__PACKAGE__->set_primary_key("uri", "branch", "revision", "isdeepclone");
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2020-02-06 12:22:36
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:0sdK9uQZpx869oqS5thRLw
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-06-19 17:26:24
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Wr0grsFTaqRlMeM9vpXjrw
 
 1;
diff --git a/src/sql/hydra.sql b/src/sql/hydra.sql
index c664d854..d3748bda 100644
--- a/src/sql/hydra.sql
+++ b/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 (
diff --git a/src/sql/upgrade-76.sql b/src/sql/upgrade-76.sql
new file mode 100644
index 00000000..0b402b2a
--- /dev/null
+++ b/src/sql/upgrade-76.sql
@@ -0,0 +1,12 @@
+-- We don't know if existing checkouts are deep clones.  This will
+-- force a new fetch (and most likely trigger a new build for deep
+-- clones, as the binary contents of '.git' are not deterministic).
+DELETE FROM CachedGitInputs;
+
+ALTER TABLE CachedGitInputs
+    ADD COLUMN isDeepClone BOOLEAN NOT NULL;
+
+ALTER TABLE CachedGitInputs DROP CONSTRAINT cachedgitinputs_pkey;
+
+ALTER TABLE CachedGitInputs ADD CONSTRAINT cachedgitinputs_pkey
+    PRIMARY KEY (uri, branch, revision, isDeepClone);