diff --git a/strix/interface/utils.py b/strix/interface/utils.py
index e051a185..f82dcdc9 100644
--- a/strix/interface/utils.py
+++ b/strix/interface/utils.py
@@ -814,6 +814,7 @@ def _classify_diff_entries(entries: list[DiffEntry]) -> dict[str, Any]:
     analyzable_files: list[str] = []
     analyzable_seen: set[str] = set()
     modified_seen: set[str] = set()
+    added_seen: set[str] = set()
 
     for entry in entries:
         path = entry.path
@@ -825,7 +826,7 @@ def _classify_diff_entries(entries: list[DiffEntry]) -> dict[str, Any]:
             continue
 
         if entry.status == "A":
-            added_files.append(path)
+            _append_unique(added_files, added_seen, path)
             _append_unique(analyzable_files, analyzable_seen, path)
             continue
 
@@ -848,7 +849,7 @@ def _classify_diff_entries(entries: list[DiffEntry]) -> dict[str, Any]:
             continue
 
         if entry.status == "C":
-            _append_unique(modified_files, modified_seen, path)
+            _append_unique(added_files, added_seen, path)
             _append_unique(analyzable_files, analyzable_seen, path)
             continue
 
@@ -1283,6 +1284,7 @@ def derive_local_base_name(path_str: str) -> str:
 
 def assign_workspace_subdirs(targets_info: list[dict[str, Any]]) -> None:
     name_counts: dict[str, int] = {}
+    allocated_subdirs: set[str] = set()
 
     for target in targets_info:
         target_type = target["type"]
@@ -1298,10 +1300,22 @@ def assign_workspace_subdirs(targets_info: list[dict[str, Any]]) -> None:
             continue
 
         count = name_counts.get(base_name, 0) + 1
-        name_counts[base_name] = count
-
         workspace_subdir = base_name if count == 1 else f"{base_name}-{count}"
 
+        # Avoid colliding with a subdir already allocated to another target
+        # (e.g. base names ["api-2", "api", "api"] would otherwise both map to "api-2").
+        # Track allocated subdirs separately from base-name counts so a derived
+        # suffix never poisons the count of a later target sharing that name.
+        max_attempts = len(targets_info) + 1
+        attempts = 0
+        while workspace_subdir in allocated_subdirs and attempts < max_attempts:
+            count += 1
+            workspace_subdir = f"{base_name}-{count}"
+            attempts += 1
+
+        name_counts[base_name] = count
+        allocated_subdirs.add(workspace_subdir)
+
         details["workspace_subdir"] = workspace_subdir
 
 
diff --git a/tests/test_diff_workspace_utils.py b/tests/test_diff_workspace_utils.py
new file mode 100644
index 00000000..2074df14
--- /dev/null
+++ b/tests/test_diff_workspace_utils.py
@@ -0,0 +1,62 @@
+"""Tests for diff classification and workspace-subdir assignment in interface.utils."""
+
+from __future__ import annotations
+
+from typing import Any
+
+from strix.interface.utils import (
+    DiffEntry,
+    _classify_diff_entries,
+    assign_workspace_subdirs,
+)
+
+
+def _local_target(path: str) -> dict[str, Any]:
+    return {"type": "local_code", "details": {"target_path": path}}
+
+
+def test_assign_workspace_subdirs_avoids_suffix_collision() -> None:
+    # Base names derive to ["api-2", "api", "api"]; the third target's naive
+    # suffix "api-2" would collide with the first, silently dropping a repo.
+    targets = [
+        _local_target("/srv/api-2"),
+        _local_target("/srv/api"),
+        _local_target("/other/api"),
+    ]
+
+    assign_workspace_subdirs(targets)
+
+    subdirs = [t["details"]["workspace_subdir"] for t in targets]
+    assert len(set(subdirs)) == 3
+    assert subdirs[0] == "api-2"
+    assert subdirs[1] == "api"
+    assert subdirs[2] not in {"api-2", "api"}
+
+
+def test_assign_workspace_subdirs_suffix_does_not_poison_later_base() -> None:
+    # Base names ["api", "api", "api-2"]: the second "api" target allocates the
+    # subdir "api-2"; the later real "api-2" target must still get a unique,
+    # non-colliding subdir without the earlier allocation poisoning its counter.
+    targets = [
+        _local_target("/srv/api"),
+        _local_target("/other/api"),
+        _local_target("/srv/api-2"),
+    ]
+
+    assign_workspace_subdirs(targets)
+
+    subdirs = [t["details"]["workspace_subdir"] for t in targets]
+    assert len(set(subdirs)) == 3
+    assert subdirs[0] == "api"
+    assert subdirs[1] == "api-2"
+    assert subdirs[2].startswith("api-2")
+
+
+def test_classify_diff_entries_copy_is_added_not_modified() -> None:
+    result = _classify_diff_entries(
+        [DiffEntry(status="C", path="new.py", old_path="orig.py", similarity=100)]
+    )
+
+    assert "new.py" in result["added_files"]
+    assert "new.py" not in result["modified_files"]
+    assert "new.py" in result["analyzable_files"]