diff --git a/src/python/merge_analyzer.py b/src/python/merge_analyzer.py
index be19c3b6d3..72280525d9 100755
--- a/src/python/merge_analyzer.py
+++ b/src/python/merge_analyzer.py
@@ -66,6 +66,7 @@ def get_diff_files(
 
 
 def diff_merge_analyzer(
+    merge_idx: str,
     repo_slug: str,
     left_sha: str,
     right_sha: str,
@@ -75,6 +76,7 @@ def diff_merge_analyzer(
     Computes the diff between two branches using git diff.
     Args:
         repo (Repository): The repository object.
+        merge_idx (str): The merge index, such as 42-123.
         repo_slug (str): The repository slug.
         left_sha (str): The left sha.
         right_sha (str): The right sha.
@@ -91,6 +93,7 @@ def diff_merge_analyzer(
         return cache_data
 
     repo = Repository(
+        merge_idx,
         repo_slug,
         cache_directory=cache_dir,
         workdir_id=repo_slug + "/diff-" + left_sha + "-" + right_sha,
@@ -149,34 +152,41 @@ def diff_merge_analyzer(
 
 
 def merge_analyzer(
-    args: Tuple[str, pd.Series, Path],
+    args: Tuple[str, str, pd.Series, Path],
 ) -> pd.Series:
     """
     Merges two branches and returns the result.
     Args:
-        args (Tuple[str,pd.Series,Path]): A tuple containing the repo slug,
+        args (Tuple[str,str,pd.Series,Path]): A tuple containing the merge index, the repo slug,
                 the merge data (which is side-effected), and the cache path.
     Returns:
         dict: A dictionary containing the merge result.
     """
-    repo_slug, merge_data, cache_directory = args
+    merge_idx, repo_slug, merge_data, cache_directory = args
 
     left_sha = merge_data["left"]
     right_sha = merge_data["right"]
 
-    logger.info(f"merge_analyzer: Analyzing {repo_slug} {left_sha} {right_sha}")
+    logger.info(
+        f"merge_analyzer: Analyzing {merge_idx} {repo_slug} {left_sha} {right_sha}"
+    )
 
     # Compute diff size in lines between left and right
-    cache_data = diff_merge_analyzer(repo_slug, left_sha, right_sha, cache_directory)
+    cache_data = diff_merge_analyzer(
+        merge_idx, repo_slug, left_sha, right_sha, cache_directory
+    )
 
     if cache_data["diff contains java file"] in (False, None):
         merge_data["test merge"] = False
         merge_data["diff contains java file"] = False
-        logger.info(f"merge_analyzer: Analyzed {repo_slug} {left_sha} {right_sha}")
+        logger.info(
+            f"merge_analyzer: Analyzed {merge_idx} {repo_slug} {left_sha} {right_sha}"
+        )
         return merge_data
 
     # Checkout left parent
     repo_left = Repository(
+        merge_idx,
         repo_slug,
         cache_directory=cache_directory,
         workdir_id=repo_slug + "/left-" + left_sha + "-" + right_sha,
@@ -185,6 +195,7 @@ def merge_analyzer(
 
     # Checkout right parent
     repo_right = Repository(
+        merge_idx,
         repo_slug,
         cache_directory=cache_directory,
         workdir_id=repo_slug + "/right-" + left_sha + "-" + right_sha,
@@ -214,15 +225,20 @@ def merge_analyzer(
         merge_data["parents pass"] and merge_data["diff contains java file"] is True
     )
 
-    logger.info(f"merge_analyzer: Analyzed {repo_slug} {left_sha} {right_sha}")
+    logger.info(
+        f"merge_analyzer: Analyzed {merge_idx} {repo_slug} {left_sha} {right_sha}"
+    )
 
     return merge_data
 
 
-def build_merge_analyzer_arguments(args: argparse.Namespace, repo_slug: str):
+def build_merge_analyzer_arguments(
+    repo_idx: str, args: argparse.Namespace, repo_slug: str
+):
     """
     Creates the arguments for the merger function.
     Args:
+        reo_idx (str): The repository index.
         args (argparse.Namespace): The arguments to the script.
         repo_slug (str): The repository slug.
     Returns:
@@ -255,8 +271,8 @@ def build_merge_analyzer_arguments(args: argparse.Namespace, repo_slug: str):
     merges["notes"] = merges["notes"].fillna("")
 
     arguments = [
-        (repo_slug, merge_data, Path(args.cache_dir))
-        for _, merge_data in merges.iterrows()
+        (f"{repo_idx}-{idx}", repo_slug, merge_data, Path(args.cache_dir))
+        for idx, merge_data in merges.iterrows()
     ]
     return arguments
 
@@ -297,9 +313,11 @@ def plot_vertical_histogram(data, title, ax):
         TimeRemainingColumn(),
     ) as progress:
         task = progress.add_task("[green]Constructing Input...", total=len(repos))
-        for _, repository_data in repos.iterrows():
+        for repo_idx, repository_data in repos.iterrows():
             repo_slug = repository_data["repository"]
-            merger_arguments += build_merge_analyzer_arguments(args, repo_slug)
+            merger_arguments += build_merge_analyzer_arguments(
+                repo_idx, args, repo_slug
+            )
             progress.update(task, advance=1)
 
     # Shuffle input to reduce cache contention
@@ -339,10 +357,10 @@ def plot_vertical_histogram(data, title, ax):
         TimeRemainingColumn(),
     ) as progress:
         task = progress.add_task("[green]Processing...", total=len(merger_arguments))
-        for idx, merge_data in enumerate(merger_arguments):
-            repo_slug = merge_data[0]
-            results_data = merger_results[idx]
-            repo_result[repo_slug].append(merger_results[idx])
+        for new_merges_idx, merge_data in enumerate(merger_arguments):
+            repo_slug = merge_data[1]
+            results_data = merger_results[new_merges_idx]
+            repo_result[repo_slug].append(merger_results[new_merges_idx])
             n_new_analyzed += 1
             if "test merge" in results_data and results_data["test merge"]:
                 n_new_candidates_to_test += 1
diff --git a/src/python/merge_runtime_measure.py b/src/python/merge_runtime_measure.py
index 3183e37a7a..52fd6ac702 100755
--- a/src/python/merge_runtime_measure.py
+++ b/src/python/merge_runtime_measure.py
@@ -63,7 +63,7 @@ def main():
             merges = merges.sample(frac=1, random_state=42)
             if len(merges) > args.n_sampled_timing:
                 merges = merges.iloc[: args.n_sampled_timing]
-            for idx, merge_data in merges.iterrows():
+            for merge_idx, merge_data in merges.iterrows():
                 for merge_tool in MERGE_TOOL:
                     left_hash, right_hash = (
                         merge_data["left"],
@@ -75,7 +75,7 @@ def main():
                     )
 
                     if cache_entry is not None:
-                        merges.at[idx, f"{merge_tool.name}_run_time"] = np.median(
+                        merges.at[merge_idx, f"{merge_tool.name}_run_time"] = np.median(
                             cache_entry["run_time"]  # type: ignore
                         )
                     else:
@@ -86,6 +86,7 @@ def main():
                         run_times = []
                         for _ in range(args.n_timings):
                             repo = Repository(
+                                merge_idx,
                                 repo_slug,
                                 workdir_id=repo_slug
                                 + f"/merge-tester-{merge_tool.name}-"
@@ -118,7 +119,7 @@ def main():
                             acquire_lock=False,
                         )
 
-                    merges.at[idx, f"{merge_tool.name}_run_time"] = np.median(
+                    merges.at[merge_idx, f"{merge_tool.name}_run_time"] = np.median(
                         cache_entry["run_time"]  # type: ignore
                     )
             out_file = args.output_dir / f"{repo_slug}.csv"
diff --git a/src/python/merge_tester.py b/src/python/merge_tester.py
index b0d8eae903..9577f93dbf 100755
--- a/src/python/merge_tester.py
+++ b/src/python/merge_tester.py
@@ -34,21 +34,25 @@
 )
 
 
-def merge_tester(args: Tuple[str, pd.Series, Path]) -> pd.Series:
+def merge_tester(args: Tuple[str, str, pd.Series, Path]) -> pd.Series:
     """Tests a merge with each merge tool.
     Args:
-        args (Tuple[str,pd.Series,Path]): A tuple containing the repository slug,
-                    the repository info, and the cache path.
+        args (Tuple[str,str,pd.Series,Path]): A tuple containing the merge index,
+                    the repository slug, the repository info, and the cache path.
     Returns:
         pd.Series: The result of the test.
     """
-    repo_slug, merge_data, cache_directory = args
+    merge_idx, repo_slug, merge_data, cache_directory = args
+    print(
+        f"merge_tester: Started {merge_idx} {repo_slug} {merge_data['left']} {merge_data['right']}"
+    )
     logger.info(
-        f"merge_tester: Started {repo_slug} {merge_data['left']} {merge_data['right']}"
+        f"merge_tester: Started {merge_idx} {repo_slug} {merge_data['left']} {merge_data['right']}"
     )
     while psutil.cpu_percent() > 90 or psutil.virtual_memory().percent > 85:
         logger.trace(
             "merge_tester: Waiting for CPU or memory to be available."
+            + merge_idx
             + repo_slug
             + merge_data["left"]
             + merge_data["right"]
@@ -57,6 +61,7 @@ def merge_tester(args: Tuple[str, pd.Series, Path]) -> pd.Series:
 
     for merge_tool in MERGE_TOOL:
         repo = Repository(
+            merge_idx,
             repo_slug,
             cache_directory=cache_directory,
             workdir_id=repo_slug
@@ -138,8 +143,8 @@ def build_arguments(
         return []
     merges = merges[merges["sampled for testing"]]
     return [
-        (repo_slug, merge_data, Path(args.cache_dir))
-        for _, merge_data in merges.iterrows()
+        (merge_idx, repo_slug, merge_data, Path(args.cache_dir))
+        for merge_idx, merge_data in merges.iterrows()
     ]
 
 
@@ -214,7 +219,7 @@ def main():
         )
         for idx, merge_results in enumerate(merge_tester_arguments):
             progress.update(task, advance=1)
-            repo_slug = merge_results[0]
+            repo_slug = merge_results[1]
             repo_result[repo_slug].append(merge_tester_results[idx])
 
     n_total_merges = 0
diff --git a/src/python/replay_merge.py b/src/python/replay_merge.py
index 8972a9eb81..5162509922 100755
--- a/src/python/replay_merge.py
+++ b/src/python/replay_merge.py
@@ -113,6 +113,7 @@ def merge_replay(
         )
         if not (WORKDIR_DIRECTORY / workdir).exists():
             repo = Repository(
+                merge_idx,
                 repo_slug,
                 cache_directory=Path("no_cache/"),
                 workdir_id=workdir,
@@ -127,6 +128,7 @@ def merge_replay(
         )
         if not (WORKDIR_DIRECTORY / workdir).exists():
             repo = Repository(
+                merge_idx,
                 repo_slug,
                 cache_directory=Path("no_cache/"),
                 workdir_id=workdir,
@@ -141,6 +143,7 @@ def merge_replay(
         )
         if not (WORKDIR_DIRECTORY / workdir).exists():
             repo = Repository(
+                merge_idx,
                 repo_slug,
                 cache_directory=Path("no_cache/"),
                 workdir_id=workdir,
@@ -164,6 +167,7 @@ def merge_replay(
         )
         if not (WORKDIR_DIRECTORY / workdir).exists():
             repo = Repository(
+                merge_idx,
                 repo_slug,
                 cache_directory=Path("no_cache/"),
                 workdir_id=workdir,
@@ -209,6 +213,7 @@ def merge_replay(
                     continue
             try:
                 repo = Repository(
+                    merge_idx,
                     repo_slug,
                     cache_directory=Path("no_cache/"),
                     workdir_id=workdir,
diff --git a/src/python/repo.py b/src/python/repo.py
index ff30633937..75c06fce1f 100755
--- a/src/python/repo.py
+++ b/src/python/repo.py
@@ -182,10 +182,13 @@ def repo_test(wcopy_dir: Path, timeout: int) -> Tuple[TEST_STATE, str]:
 
 
 class Repository:
-    """A class that represents a repository."""
+    """A class that represents a repository.
+    merge_idx is purely for diagnostic purposes.
+    """
 
     def __init__(
         self,
+        merge_idx: str,
         repo_slug: str,
         cache_directory: Path = Path(""),
         workdir_id: str = uuid.uuid4().hex,  # uuid4 is a random UID
@@ -197,6 +200,7 @@ def __init__(
             repo_slug (str): The slug of the repository, which is "owner/reponame".
             cache_directory (Path): The prefix of the cache.
         """
+        self.merge_idx = merge_idx
         self.repo_slug = repo_slug.lower()
         self.owner, self.name = self.repo_slug.split("/")
         self.repo_path = REPOS_PATH / repo_slug
diff --git a/src/python/test_repo_heads.py b/src/python/test_repo_heads.py
index 61f4129e5e..ee6769a4cc 100755
--- a/src/python/test_repo_heads.py
+++ b/src/python/test_repo_heads.py
@@ -72,6 +72,7 @@ def head_passes_tests(args: Tuple[pd.Series, Path]) -> pd.Series:
     # Load repo
     try:
         repo = Repository(
+            "HEAD",
             repo_slug,
             cache_directory=cache,
             workdir_id=repo_slug + "/head-" + repo_info["repository"],
diff --git a/src/python/write_head_hashes.py b/src/python/write_head_hashes.py
index a0243aa1ff..37a4f0e2e6 100755
--- a/src/python/write_head_hashes.py
+++ b/src/python/write_head_hashes.py
@@ -48,6 +48,7 @@ def get_latest_hash(args):
     try:
         logger.info("write_head_hashes " + repo_slug + " : Cloning repo")
         repo = Repository(
+            "HEAD",
             repo_slug,
             workdir_id=repo_slug + "/head-" + repo_slug,
             lazy_clone=False,