From 0faae74a4452bdbc0bd9f94e67eb6062fae31cd0 Mon Sep 17 00:00:00 2001
From: David Zuckerman <dzuckerm@berkeley.edu>
Date: Tue, 30 Jun 2026 14:55:16 -0700
Subject: [PATCH 1/2] Skipped excluded and hidden files for file copy

---
 mokelumne/util/file_transfer.py | 35 ++++++++++++++++++++++++---------
 test/unit/test_file_transfer.py | 26 ++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 9 deletions(-)

diff --git a/mokelumne/util/file_transfer.py b/mokelumne/util/file_transfer.py
index d8b4f5b..a0f5eb3 100644
--- a/mokelumne/util/file_transfer.py
+++ b/mokelumne/util/file_transfer.py
@@ -20,19 +20,36 @@ def sha256_for_file(path: Path) -> str:
     return sha256.hexdigest()
 
 
+def _should_include_manifest_entry(source_path: Path, item: Path) -> bool:
+    """Return True when a path should be added to the manifest."""
+    relative_path = item.relative_to(source_path)
+
+    if any(part.startswith(".") for part in relative_path.parts):
+        return False
+
+    if item.name.casefold() in {"thumbs.db", ".ds_store"}:
+        return False
+
+    return True
+
 def build_file_manifest(source_path: Path) -> Manifest:
     files = []
 
     for item in source_path.rglob("*"):
-        if item.is_file():
-            relative_path = item.relative_to(source_path)
-            files.append(
-                {
-                    "path": str(relative_path),
-                    "size": item.stat().st_size,
-                    "sha256": sha256_for_file(item),
-                }
-            )
+        if not item.is_file():
+            continue
+
+        if not _should_include_manifest_entry(source_path, item):
+            continue
+
+        relative_path = item.relative_to(source_path)
+        files.append(
+            {
+                "path": str(relative_path),
+                "size": item.stat().st_size,
+                "sha256": sha256_for_file(item),
+            }
+        )
     
     return {
         "source_root": str(source_path),
diff --git a/test/unit/test_file_transfer.py b/test/unit/test_file_transfer.py
index dd6b40b..53be53c 100644
--- a/test/unit/test_file_transfer.py
+++ b/test/unit/test_file_transfer.py
@@ -69,6 +69,32 @@ def test_build_manifest_includes_nested_files(self, tmp_path: Path):
         }
         assert len(result) == 2
 
+    def test_build_manifest_excludes_hidden_and_excluded_files(self, tmp_path: Path):
+        """Ensure that build_manifest skips hidden and system junk files."""
+        visible_file = tmp_path / "visible.tif"
+        visible_file.write_text("hello", encoding="utf-8")
+
+        hidden_file = tmp_path / ".hidden.txt"
+        hidden_file.write_text("secret", encoding="utf-8")
+
+        hidden_dir = tmp_path / ".hidden"
+        hidden_dir.mkdir()
+        hidden_dir_file = hidden_dir / "nested.txt"
+        hidden_dir_file.write_text("nested", encoding="utf-8")
+
+        ds_store = tmp_path / ".DS_Store"
+        ds_store.write_text("folder metadata", encoding="utf-8")
+
+        thumbs_db = tmp_path / "Thumbs.db"
+        thumbs_db.write_text("thumbnail images db", encoding="utf-8")
+
+        result = file_transfer.build_file_manifest(tmp_path)
+
+        paths = {entry["path"] for entry in result["files"]}
+
+        assert paths == {"visible.tif"}
+        assert len(result["files"]) == 1
+
     def test_verify_manifest_success(self, tmp_path: Path):
         """Ensure verify_manifest succeeds for valid files."""
 

From 7483e1bbcda167297e2c8a3e852873dcafb8abef Mon Sep 17 00:00:00 2001
From: David Zuckerman <dzuckerm@berkeley.edu>
Date: Tue, 30 Jun 2026 15:26:41 -0700
Subject: [PATCH 2/2] refactored so relative path isn't created twice in
 file_transfer.py

---
 mokelumne/util/file_transfer.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/mokelumne/util/file_transfer.py b/mokelumne/util/file_transfer.py
index a0f5eb3..e26604c 100644
--- a/mokelumne/util/file_transfer.py
+++ b/mokelumne/util/file_transfer.py
@@ -20,14 +20,12 @@ def sha256_for_file(path: Path) -> str:
     return sha256.hexdigest()
 
 
-def _should_include_manifest_entry(source_path: Path, item: Path) -> bool:
+def _should_include_manifest_entry(relative_path: Path, item: Path) -> bool:
     """Return True when a path should be added to the manifest."""
-    relative_path = item.relative_to(source_path)
-
     if any(part.startswith(".") for part in relative_path.parts):
         return False
 
-    if item.name.casefold() in {"thumbs.db", ".ds_store"}:
+    if item.name.casefold() in {"thumbs.db"}:
         return False
 
     return True
@@ -39,10 +37,10 @@ def build_file_manifest(source_path: Path) -> Manifest:
         if not item.is_file():
             continue
 
-        if not _should_include_manifest_entry(source_path, item):
+        relative_path = item.relative_to(source_path)
+        if not _should_include_manifest_entry(relative_path, item):
             continue
 
-        relative_path = item.relative_to(source_path)
         files.append(
             {
                 "path": str(relative_path),