Add deploy refs for currently deployed commit.

When we deploy e.g. app/org.foo.bar/x86_64/stable, then we
also create a deploy/app/org.foo.bar/x86_64/stable ref pointing to
the latest deployed commit. We also remove it when an app is uninstalled.

This means that a prune operation will not delete objects that are deployed
(which would not save any space anyway). This is nice because this can
happen for instance when you flatpak update --no-deploy.

Fixes https://github.com/flatpak/flatpak/issues/2085

Closes: #2563
Approved by: alexlarsson

common/flatpak-dir.c

@@ -6846,6 +6846,22 @@ apply_extra_data (FlatpakDir   *self,
   return TRUE;
 }
 
+/* We create a deploy ref for the currently deployed version of all refs to avoid
+   deployed commits being pruned when e.g. we pull --no-deploy. */
+static gboolean
+flatpak_dir_update_deploy_ref (FlatpakDir          *self,
+                               const char          *ref,
+                               const char          *checksum,
+                               GError             **error)
+{
+  g_autofree char *deploy_ref = g_strconcat ("deploy/", ref, NULL);
+
+  if (!ostree_repo_set_ref_immediate (self->repo, NULL, deploy_ref, checksum, NULL, error))
+    return FALSE;
+
+  return TRUE;
+}
+
 gboolean
 flatpak_dir_deploy (FlatpakDir          *self,
                     const char          *origin,
@@ -7280,6 +7296,9 @@ flatpak_dir_deploy (FlatpakDir          *self,
   if (!flatpak_dir_set_active (self, ref, checkout_basename, cancellable, error))
     return FALSE;
 
+  if (!flatpak_dir_update_deploy_ref (self, ref, checksum, error))
+    return FALSE;
+
   return TRUE;
 }
 
@@ -8600,6 +8619,9 @@ flatpak_dir_uninstall (FlatpakDir                 *self,
         }
     }
 
+  if (!flatpak_dir_update_deploy_ref (self, ref, NULL, error))
+    return FALSE;
+
   if (!flatpak_dir_undeploy_all (self, ref, force_remove, &was_deployed, cancellable, error))
     return FALSE;