Preserve checkout safety and conflict staging during pull

minigit/index.py

@@ -374,10 +374,21 @@ def _working_status(self) -> DiffResult:
 
         return result
 
-    def checkout(self, tree_hash) -> None:
+    def checkout(self, tree_hash, conflicted_paths=()) -> None:
+        """Make the working files and the index match `tree_hash`.
+
+        `conflicted_paths` (used by a merge) are written to disk like every other
+        path - their blob in the tree holds the conflict markers - but their index
+        entry stays at its pre-merge version (or is left out if there was none), so
+        status reports them as "not staged" until `add` resolves them.
+        """
         target_entries = self.read_tree_entries(tree_hash)
         target_by_path = {e.path: e for e in target_entries}
 
+        conflicted = set(conflicted_paths)
+        for path in sorted(conflicted - set(target_by_path)):
+            raise MiniGitError(f"conflicted path is not in the target tree: {path}")
+
         # Reject unsafe paths
         blob_cache = {}
         for entry in target_entries:
@@ -451,8 +462,14 @@ def checkout(self, tree_hash) -> None:
                 f.write(blob_cache[entry.path])
             os.chmod(full_path, 0o755 if entry.mode == "100755" else 0o644)
 
-        # Now matched
-        self.write_index(target_entries)
+        # Now matched - except conflicted paths, which keep their pre-merge entry.
+        index_entries = []
+        for entry in target_entries:
+            if entry.path not in conflicted:
+                index_entries.append(entry)
+            elif entry.path in current_by_path:
+                index_entries.append(current_by_path[entry.path])
+        self.write_index(index_entries)
 
     def _validate_checkout_path(self, path: str) -> None:
         if (