fix(backup): stage SQLite snapshots alongside output zip and stop excluding nested hermes-agent skill dirs

Two bugs in the backup routine:

1. SQLite safe-copy used tempfile.NamedTemporaryFile() which defaults to
   the system temp directory (/tmp).  When /tmp is a small tmpfs and the
   database is large, the copy silently fails and the resulting zip is
   missing state.db, kanban.db, and response_store.db.

   Fix: pass dir=out_path.parent so the temp file is staged alongside the
   output zip on the same filesystem.

2. _EXCLUDED_DIRS contained "hermes-agent" which matched at ANY path
   depth, accidentally excluding the Hermes Agent skill directory at
   skills/autonomous-ai-agents/hermes-agent/.

   Fix: special-case "hermes-agent" to only match when it is the first
   path component (the root-level code checkout).  All other excluded dir
   names continue to match at any depth.

Regression tests added for both fixes.

hermes_cli/backup.py

@@ -31,6 +31,9 @@ logger = logging.getLogger(__name__)
 # ---------------------------------------------------------------------------
 
 # Directory names to skip entirely (matched against each path component)
+# ``hermes-agent`` is special-cased to root level only in ``_should_exclude``
+# so that skill directories like ``skills/autonomous-ai-agents/hermes-agent/``
+# are not accidentally excluded.
 _EXCLUDED_DIRS = {
     "hermes-agent",     # the codebase repo — re-clone instead
     "__pycache__",      # bytecode caches — regenerated on import
@@ -69,10 +72,15 @@ def _should_exclude(rel_path: Path) -> bool:
     """Return True if *rel_path* (relative to hermes root) should be skipped."""
     parts = rel_path.parts
 
-    # Any path component matches an excluded dir name
     for part in parts:
-        if part in _EXCLUDED_DIRS:
-            return True
+        if part not in _EXCLUDED_DIRS:
+            continue
+        # ``hermes-agent`` only matches at the root level (first component).
+        # Nested directories with the same name — e.g.
+        # ``skills/autonomous-ai-agents/hermes-agent/`` — must be preserved.
+        if part == "hermes-agent" and part != parts[0]:
+            continue
+        return True
 
     name = rel_path.name
 
@@ -177,10 +185,13 @@ def run_backup(args) -> None:
         rel_dir = dp.relative_to(hermes_root)
 
         # Prune excluded directories in-place so os.walk doesn't descend
+        # ``hermes-agent`` is only pruned at the root level; nested dirs
+        # with the same name (e.g. in skills/) must be preserved.
+        is_root = rel_dir == Path(".")
         orig_dirnames = dirnames[:]
         dirnames[:] = [
             d for d in dirnames
-            if d not in _EXCLUDED_DIRS
+            if d not in _EXCLUDED_DIRS or (d == "hermes-agent" and not is_root)
         ]
         for removed in set(orig_dirnames) - set(dirnames):
             skipped_dirs.add(str(rel_dir / removed))
@@ -211,7 +222,13 @@ def run_backup(args) -> None:
             try:
                 # Safe copy for SQLite databases (handles WAL mode)
                 if abs_path.suffix == ".db":
-                    with tempfile.NamedTemporaryFile(suffix=".db", delete=False) as tmp:
+                    # Stage the snapshot alongside the output zip so that the
+                    # temp file lives on the same filesystem.  The system
+                    # default (/tmp) may be a small tmpfs that cannot hold
+                    # large databases, causing silent backup incompleteness.
+                    with tempfile.NamedTemporaryFile(
+                        suffix=".db", delete=False, dir=str(out_path.parent)
+                    ) as tmp:
                         tmp_db = Path(tmp.name)
                     if _safe_copy_db(abs_path, tmp_db):
                         zf.write(tmp_db, arcname=str(rel_path))

tests/hermes_cli/test_backup.py

@@ -146,6 +146,12 @@ class TestShouldExclude:
         from hermes_cli.backup import _should_exclude
         assert not _should_exclude(Path("logs/agent.log"))
 
+    def test_includes_nested_hermes_agent_in_skills(self):
+        """skills/autonomous-ai-agents/hermes-agent/ must NOT be excluded —
+        only the root-level hermes-agent/ repo is skipped."""
+        from hermes_cli.backup import _should_exclude
+        assert not _should_exclude(Path("skills/autonomous-ai-agents/hermes-agent/SKILL.md"))
+        assert not _should_exclude(Path("skills/autonomous-ai-agents/hermes-agent/sub/item.txt"))
 
 # ---------------------------------------------------------------------------
 # Backup tests
@@ -206,6 +212,37 @@ class TestBackup:
             agent_files = [n for n in names if "hermes-agent" in n]
             assert agent_files == [], f"hermes-agent files leaked into backup: {agent_files}"
 
+    def test_includes_nested_hermes_agent_in_skills(self, tmp_path, monkeypatch):
+        """Backup includes skills/.../hermes-agent/ but NOT root hermes-agent/."""
+        hermes_home = tmp_path / ".hermes"
+        hermes_home.mkdir()
+        _make_hermes_tree(hermes_home)
+
+        # Add a nested hermes-agent directory inside skills (like the real layout)
+        nested = hermes_home / "skills" / "autonomous-ai-agents" / "hermes-agent"
+        nested.mkdir(parents=True)
+        (nested / "SKILL.md").write_text("# Hermes Agent Skill\n")
+        (nested / "sub").mkdir()
+        (nested / "sub" / "item.txt").write_text("nested content\n")
+
+        monkeypatch.setenv("HERMES_HOME", str(hermes_home))
+        monkeypatch.setattr(Path, "home", lambda: tmp_path)
+
+        out_zip = tmp_path / "backup.zip"
+        args = Namespace(output=str(out_zip))
+
+        from hermes_cli.backup import run_backup
+        run_backup(args)
+
+        with zipfile.ZipFile(out_zip, "r") as zf:
+            names = zf.namelist()
+            # Root hermes-agent must be excluded
+            root_agent = [n for n in names if n.startswith("hermes-agent/")]
+            assert root_agent == [], f"root hermes-agent leaked: {root_agent}"
+            # Nested skill hermes-agent must be included
+            assert "skills/autonomous-ai-agents/hermes-agent/SKILL.md" in names
+            assert "skills/autonomous-ai-agents/hermes-agent/sub/item.txt" in names
+
     def test_excludes_pycache(self, tmp_path, monkeypatch):
         """Backup does NOT include __pycache__ dirs."""
         hermes_home = tmp_path / ".hermes"