diff --git a/src/python/merge_analyzer.py b/src/python/merge_analyzer.py
index 42f7d1d6aa..1360584f12 100755
--- a/src/python/merge_analyzer.py
+++ b/src/python/merge_analyzer.py
@@ -42,7 +42,7 @@ def merge_analyzer(  # pylint: disable=too-many-locals
     Merges two branches and returns the result.
     Args:
         args (Tuple[str,pd.Series,Path]): A tuple containing the repo slug,
-                the merge data, and the cache path.
+                the merge data (which is side-effected), and the cache path.
     Returns:
         dict: A dictionary containing the merge result.
     """
@@ -58,8 +58,12 @@ def merge_analyzer(  # pylint: disable=too-many-locals
         return merge_data
 
     cache_data = {}
-    repo_left = Repository(repo_slug, cache_directory=cache_directory)
-    repo_right = Repository(repo_slug, cache_directory=cache_directory)
+    repo_left = Repository(
+        repo_slug, cache_directory=cache_directory, workdir_id=merge_data["left"]
+    )
+    repo_right = Repository(
+        repo_slug, cache_directory=cache_directory, workdir_id=merge_data["right"]
+    )
     left_success, _ = repo_left.checkout(merge_data["left"])
     right_success, _ = repo_right.checkout(merge_data["right"])
 
diff --git a/src/python/merge_differ.py b/src/python/merge_differ.py
index cd8e3a60fa..6a269d38cc 100755
--- a/src/python/merge_differ.py
+++ b/src/python/merge_differ.py
@@ -51,7 +51,11 @@ def get_merge_fingerprint(
         return None, None
     left = merge_data["left"]
     right = merge_data["right"]
-    repo = Repository(repo_slug, cache_directory=cache_directory)
+    repo = Repository(
+        repo_slug,
+        cache_directory=cache_directory,
+        workdir_id="merge-" + left + "-" + right,
+    )
     (
         merge_status,
         merge_fingerprint,
diff --git a/src/python/merge_tester.py b/src/python/merge_tester.py
index 9564194091..528453e6d0 100755
--- a/src/python/merge_tester.py
+++ b/src/python/merge_tester.py
@@ -52,7 +52,9 @@ def merge_tester(args: Tuple[str, pd.Series, Path]) -> pd.Series:
     merge_data["parents pass"] = False
     for branch in ["left", "right"]:
         commit_sha = merge_data[branch]
-        repo = Repository(repo_slug, cache_directory=cache_directory)
+        repo = Repository(
+            repo_slug, cache_directory=cache_directory, workdir_id=commit_sha
+        )
         test_result, test_coverage, tree_fingerprint = repo.checkout_and_test(
             commit_sha, TIMEOUT_TESTING_PARENT, N_TESTS
         )
@@ -77,7 +79,11 @@ def merge_tester(args: Tuple[str, pd.Series, Path]) -> pd.Series:
     merge_data["parents pass"] = True
 
     for merge_tool in MERGE_TOOL:
-        repo = Repository(repo_slug, cache_directory=cache_directory)
+        repo = Repository(
+            repo_slug,
+            cache_directory=cache_directory,
+            workdir_id="merge-" + merge_data["left"] + "-" + merge_data["right"],
+        )
         (
             result,
             merge_fingerprint,
diff --git a/src/python/repo.py b/src/python/repo.py
index fddbfaa952..1922897b1c 100755
--- a/src/python/repo.py
+++ b/src/python/repo.py
@@ -113,6 +113,7 @@ def __init__(
         self,
         repo_slug: str,
         cache_directory: Path = Path(""),
+        workdir_id=uuid.uuid4().hex,  # uuid4 is a random UID
     ) -> None:
         """Initializes the repository.
         Args:
@@ -121,7 +122,6 @@ def __init__(
         """
         self.repo_slug = repo_slug
         self.path = REPOS_PATH / repo_slug.split("/")[1]
-        workdir_id = uuid.uuid4().hex
         self.workdir = WORKDIR_DIRECTORY / workdir_id
         self.workdir.mkdir(parents=True, exist_ok=True)
         self.repo_path = self.workdir / self.path.name
diff --git a/src/python/test_repo_heads.py b/src/python/test_repo_heads.py
index 1fa8bca13b..cff1b1cbfb 100755
--- a/src/python/test_repo_heads.py
+++ b/src/python/test_repo_heads.py
@@ -42,7 +42,9 @@ def head_passes_tests(args: Tuple[pd.Series, Path]) -> TEST_STATE:
     repo_slug = repo_info["repository"]
     print("test_repo_heads:", repo_slug, ": head_passes_tests : started")
 
-    repo = Repository(repo_slug, cache_directory=cache)
+    repo = Repository(
+        repo_slug, cache_directory=cache, workdir_id="head-" + repo_info["head hash"]
+    )
     test_state, _, _ = repo.checkout_and_test(
         repo_info["head hash"], timeout=TIMEOUT_TESTING, n_tests=3
     )