fix(#4783): prune dependency trees in mtime probe to match compute path (gate finding 4)

Codex round-4 found my followlinks=True change introduced a perf regression: the
probe os.walk lacked the .git/.venv/node_modules/site-packages + skill-support-dir
pruning that iter_skill_index_files applies, so a skill vendoring a dependency
tree made this EVERY-CALL probe walk thousands of irrelevant files — defeating the
cache's whole purpose. The probe now prunes dirnames[:] with the same
EXCLUDED_SKILL_DIRS + SKILL_SUPPORT_DIRS sets as the compute path. Regression test
(change deep inside node_modules/ must not move the probe) added + non-vacuous.

Co-authored-by: Rod Boev <rod.boev@gmail.com>

api/profiles.py

@@ -1595,6 +1595,11 @@ def _skill_tree_max_mtime_ns(skills_dir: Path, config_path: Path) -> int:
         pass
     if not skills_dir.is_dir():
         return max_ns
+    try:
+        from agent.skill_utils import EXCLUDED_SKILL_DIRS, SKILL_SUPPORT_DIRS
+    except Exception:
+        EXCLUDED_SKILL_DIRS = frozenset()
+        SKILL_SUPPORT_DIRS = frozenset()
     try:
         # Directory mtimes catch nested out-of-band deletes that leave file mtimes unchanged.
         # followlinks=True mirrors agent.skill_utils.iter_skill_index_files (the compute
@@ -1602,6 +1607,16 @@ def _skill_tree_max_mtime_ns(skills_dir: Path, config_path: Path) -> int:
         # SKILL.md change the probe value — otherwise such edits would stay stale up to the TTL.
         for root, dirnames, filenames in os.walk(skills_dir, followlinks=True):
             root_path = Path(root)
+            # Prune the SAME trees iter_skill_index_files prunes (.git/.venv/
+            # node_modules/site-packages + skill support dirs), so a skill that
+            # vendors a dependency tree doesn't make this every-call probe walk
+            # thousands of irrelevant files and defeat the cache's perf goal.
+            has_skill_md = "SKILL.md" in filenames
+            dirnames[:] = [
+                d for d in dirnames
+                if d not in EXCLUDED_SKILL_DIRS
+                and not (has_skill_md and d in SKILL_SUPPORT_DIRS)
+            ]
             try:
                 max_ns = max(max_ns, root_path.stat().st_mtime_ns)
             except OSError:

tests/test_issue4783_profile_skills_mtime_cache.py

@@ -343,6 +343,35 @@ class TestSymlinkedSkillProbeFollowsLinks:
             "probe must follow the symlinked skill dir and see the target SKILL.md mtime change"
         )
 
+    def test_probe_prunes_dependency_trees_like_compute_path(self, profiles_mod):
+        """The probe must NOT descend into pruned trees (.venv/node_modules/
+        site-packages/support dirs) — matching iter_skill_index_files — so a
+        skill that vendors a dependency tree doesn't make this every-call probe
+        walk thousands of irrelevant files. A mtime change DEEP inside a pruned
+        dir must NOT move the probe value (it's not part of the skill index)."""
+        mod, profile_dir = profiles_mod
+        skills_dir = profile_dir / "skills"
+        skill = skills_dir / "vendored"
+        skill.mkdir(parents=True)
+        (skill / "SKILL.md").write_text("---\nname: vendored\n---\n# vendored\n", encoding="utf-8")
+        # A vendored dependency tree that the compute path prunes.
+        buried = skill / "node_modules" / "pkg"
+        buried.mkdir(parents=True)
+        buried_file = buried / "index.js"
+        buried_file.write_text("// dep\n", encoding="utf-8")
+
+        before = mod._skill_tree_max_mtime_ns(skills_dir, profile_dir / "config.yaml")
+        import os as _os
+        future = time.time() + 1000
+        _os.utime(buried_file, (future, future))
+        _os.utime(buried, (future, future))
+        after = mod._skill_tree_max_mtime_ns(skills_dir, profile_dir / "config.yaml")
+
+        assert after == before, (
+            "probe must prune node_modules/ (not descend) — a change inside a pruned "
+            f"dependency tree must not move the probe value (before={before}, after={after})"
+        )
+
 
 class TestReturnSignature:
     """Proof matrix row 6: return signature is tuple[int, int]."""