fix(backup): don't stage targets for skipped missing-source items

src/argit/backup.py

@@ -537,7 +537,13 @@ def _git_commit(
     for it in concrete_items:
         if it.kind == "secret":
             continue  # secret is in secrets/, added below
-        if it.target:
+        # Stage only targets that were actually written. An item whose source
+        # is absent on this agent is skipped during copy (§4-7), so its target
+        # never exists; staging it anyway makes `git add` abort the whole backup
+        # with "pathspec '<target>' did not match any files". This happens
+        # whenever the live agent lacks a path the bundled manifest declares
+        # (e.g. a 2026.5.4 manifest against a 2026.5.7 Hermes build).
+        if it.target and (repo_root / it.target).exists():
             paths_to_add.append(it.target)
     for sf in manifest.sanitize:
         paths_to_add.append(sf.target)

tests/unit/test_backup_review_staging.py

@@ -14,7 +14,7 @@
 from unittest.mock import patch
 
 from argit.backup import _git_commit
-from argit.manifest import Manifest
+from argit.manifest import Item, Manifest
 
 
 def _empty_manifest() -> Manifest:
@@ -87,3 +87,31 @@ def test_git_commit_omits_review_path_when_none(capsys, tmp_path):
     )
     captured = capsys.readouterr()
     assert ".argit/reviews/" not in captured.out
+
+
+def test_git_commit_skips_items_with_missing_target(capsys, tmp_path):
+    """An item whose source was absent is skipped during copy, so its target is
+    never written. _git_commit must NOT stage that target — otherwise `git add`
+    fails with "pathspec did not match any files" and aborts the whole backup.
+    (Reproduces a 2026.5.4 manifest declaring scripts/ against a Hermes build
+    that has no ~/.hermes/scripts/.)"""
+    repo = tmp_path / "repo"
+    (repo / "hermes" / "data").mkdir(parents=True)
+    # present: copied this run, target exists on disk
+    present_tgt = repo / "hermes" / "data" / "config.yaml"
+    present_tgt.write_text("model: x\n")
+    present = Item(kind="data", source="config.yaml", mode="0644",
+                   target="hermes/data/config.yaml")
+    # missing: source absent → skipped during copy → target never written
+    missing = Item(kind="data", source="scripts/", mode="0755",
+                   target="hermes/data/scripts/")
+
+    _git_commit(
+        repo, _empty_manifest(),
+        concrete_items=[present, missing], iso="2026-06-10T00:00:00Z",
+        dry=True, review_path=None,
+    )
+
+    out = capsys.readouterr().out
+    assert "hermes/data/config.yaml" in out
+    assert "hermes/data/scripts/" not in out