diff --git a/recipe_modules/checkout/api.py b/recipe_modules/checkout/api.py
index 444af57..f7507c8 100644
--- a/recipe_modules/checkout/api.py
+++ b/recipe_modules/checkout/api.py
@@ -1564,12 +1564,13 @@
 
             self._workspace(ctx)
 
-            with self.m.context(cwd=ctx.root):
-                self.m.git.clean(force=2, recursive=True)
-                try:
-                    self.m.git.status()
-                except self.m.step.StepFailure:  # pragma: no cover
-                    pass
+            if not options.use_repo:
+                with self.m.context(cwd=ctx.root):
+                    self.m.git.clean(force=2, recursive=True)
+                    try:
+                        self.m.git.status()
+                    except self.m.step.StepFailure:  # pragma: no cover
+                        pass
 
             ctx.status = self._check_unapplied_changes(ctx.changes)
 
diff --git a/recipe_modules/checkout/tests/repo.expected/ci.json b/recipe_modules/checkout/tests/repo.expected/ci.json
index a991c75..f36cf80 100644
--- a/recipe_modules/checkout/tests/repo.expected/ci.json
+++ b/recipe_modules/checkout/tests/repo.expected/ci.json
@@ -731,33 +731,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/feature_branches_ci.json b/recipe_modules/checkout/tests/repo.expected/feature_branches_ci.json
index 5785a0d..22983f5 100644
--- a/recipe_modules/checkout/tests/repo.expected/feature_branches_ci.json
+++ b/recipe_modules/checkout/tests/repo.expected/feature_branches_ci.json
@@ -1043,57 +1043,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:ci"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:ci"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/feature_branches_try.json b/recipe_modules/checkout/tests/repo.expected/feature_branches_try.json
index 4470318..bfbb400 100644
--- a/recipe_modules/checkout/tests/repo.expected/feature_branches_try.json
+++ b/recipe_modules/checkout/tests/repo.expected/feature_branches_try.json
@@ -1206,57 +1206,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/feature_branches_try_multiple_features.json b/recipe_modules/checkout/tests/repo.expected/feature_branches_try_multiple_features.json
index 28926ca..4723f98 100644
--- a/recipe_modules/checkout/tests/repo.expected/feature_branches_try_multiple_features.json
+++ b/recipe_modules/checkout/tests/repo.expected/feature_branches_try_multiple_features.json
@@ -1656,57 +1656,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/feature_branches_try_no_matching.json b/recipe_modules/checkout/tests/repo.expected/feature_branches_try_no_matching.json
index e709bf7..67cd52c 100644
--- a/recipe_modules/checkout/tests/repo.expected/feature_branches_try_no_matching.json
+++ b/recipe_modules/checkout/tests/repo.expected/feature_branches_try_no_matching.json
@@ -1565,57 +1565,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/no_trigger.json b/recipe_modules/checkout/tests/repo.expected/no_trigger.json
index cdf3d90..6703e52 100644
--- a/recipe_modules/checkout/tests/repo.expected/no_trigger.json
+++ b/recipe_modules/checkout/tests/repo.expected/no_trigger.json
@@ -728,33 +728,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/prefix.json b/recipe_modules/checkout/tests/repo.expected/prefix.json
index b4fb109..e4c5a8e 100644
--- a/recipe_modules/checkout/tests/repo.expected/prefix.json
+++ b/recipe_modules/checkout/tests/repo.expected/prefix.json
@@ -1153,57 +1153,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/try-multiple-cqdeps.json b/recipe_modules/checkout/tests/repo.expected/try-multiple-cqdeps.json
index ad190fb..2b3a0f1 100644
--- a/recipe_modules/checkout/tests/repo.expected/try-multiple-cqdeps.json
+++ b/recipe_modules/checkout/tests/repo.expected/try-multiple-cqdeps.json
@@ -1796,57 +1796,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/try-multiple-onenotapplied.json b/recipe_modules/checkout/tests/repo.expected/try-multiple-onenotapplied.json
index 9bba215..292e2fd 100644
--- a/recipe_modules/checkout/tests/repo.expected/try-multiple-onenotapplied.json
+++ b/recipe_modules/checkout/tests/repo.expected/try-multiple-onenotapplied.json
@@ -1642,57 +1642,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.some changes were not applied",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/try-multiple.json b/recipe_modules/checkout/tests/repo.expected/try-multiple.json
index adfbe83..9e6d87c 100644
--- a/recipe_modules/checkout/tests/repo.expected/try-multiple.json
+++ b/recipe_modules/checkout/tests/repo.expected/try-multiple.json
@@ -1567,57 +1567,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/try.json b/recipe_modules/checkout/tests/repo.expected/try.json
index a00cf20..709fcb5 100644
--- a/recipe_modules/checkout/tests/repo.expected/try.json
+++ b/recipe_modules/checkout/tests/repo.expected/try.json
@@ -1157,57 +1157,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/try_manifest.json b/recipe_modules/checkout/tests/repo.expected/try_manifest.json
index 9b6d592..57044f4 100644
--- a/recipe_modules/checkout/tests/repo.expected/try_manifest.json
+++ b/recipe_modules/checkout/tests/repo.expected/try_manifest.json
@@ -1225,57 +1225,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co/foo",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [
diff --git a/recipe_modules/checkout/tests/repo.expected/try_repo_not_in_manifest.json b/recipe_modules/checkout/tests/repo.expected/try_repo_not_in_manifest.json
index 0d9e188..1ab20ca 100644
--- a/recipe_modules/checkout/tests/repo.expected/try_repo_not_in_manifest.json
+++ b/recipe_modules/checkout/tests/repo.expected/try_repo_not_in_manifest.json
@@ -815,57 +815,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:try"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.no changes were applied",
     "~followup_annotations": [
diff --git a/recipes/target_to_cipd.expected/success.json b/recipes/target_to_cipd.expected/success.json
index 80247cd..5b461fd 100644
--- a/recipes/target_to_cipd.expected/success.json
+++ b/recipes/target_to_cipd.expected/success.json
@@ -1007,57 +1007,6 @@
     ]
   },
   {
-    "cmd": [
-      "git",
-      "clean",
-      "-f",
-      "-f",
-      "-d"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:ci"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git clean",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
-    "cmd": [
-      "git",
-      "status"
-    ],
-    "cwd": "[START_DIR]/co",
-    "luci_context": {
-      "realm": {
-        "name": "project:ci"
-      },
-      "resultdb": {
-        "current_invocation": {
-          "name": "invocations/build:8945511751514863184",
-          "update_token": "token"
-        },
-        "hostname": "rdbhost"
-      }
-    },
-    "name": "checkout pigweed.git status",
-    "timeout": 600.0,
-    "~followup_annotations": [
-      "@@@STEP_NEST_LEVEL@1@@@"
-    ]
-  },
-  {
     "cmd": [],
     "name": "checkout pigweed.status",
     "~followup_annotations": [