diff --git a/agent/prompt_builder.py b/agent/prompt_builder.py
index a9556e204688..54a21635a74c 100644
--- a/agent/prompt_builder.py
+++ b/agent/prompt_builder.py
@@ -5,6 +5,7 @@
 """
 
 import json
+import hashlib
 import logging
 import os
 import re
@@ -588,6 +589,22 @@ def _build_skills_manifest(skills_dir: Path) -> dict[str, list[int]]:
     return manifest
 
 
+def _skills_manifest_digest(skills_dir: Path) -> str:
+    """Return a stable digest of one skills directory's manifest."""
+    manifest = _build_skills_manifest(skills_dir)
+    payload = json.dumps(manifest, sort_keys=True, separators=(",", ":"))
+    return hashlib.sha1(payload.encode("utf-8")).hexdigest()
+
+
+def _skills_cache_state(skills_dir: Path, external_dirs: list[Path]) -> tuple[tuple[str, str], ...]:
+    """Return cache state tokens for local + external skill directories."""
+    dirs = [skills_dir, *external_dirs]
+    return tuple(
+        (str(directory.resolve()), _skills_manifest_digest(directory))
+        for directory in dirs
+    )
+
+
 def _load_skills_snapshot(skills_dir: Path) -> Optional[dict]:
     """Load the disk snapshot if it exists and its manifest still matches."""
     snapshot_path = _skills_prompt_snapshot_path()
@@ -745,7 +762,7 @@ def build_skills_system_prompt(
     disabled = get_disabled_skill_names()
     cache_key = (
         str(skills_dir.resolve()),
-        tuple(str(d) for d in external_dirs),
+        _skills_cache_state(skills_dir, external_dirs),
         tuple(sorted(str(t) for t in (available_tools or set()))),
         tuple(sorted(str(ts) for ts in (available_toolsets or set()))),
         _platform_hint,
diff --git a/tests/agent/test_prompt_builder.py b/tests/agent/test_prompt_builder.py
index 88de5186b838..337e1a063468 100644
--- a/tests/agent/test_prompt_builder.py
+++ b/tests/agent/test_prompt_builder.py
@@ -372,6 +372,28 @@ def test_rebuilds_prompt_when_disabled_skills_change(self, monkeypatch, tmp_path
         second = build_skills_system_prompt()
         assert "cached-skill" not in second
 
+    def test_rebuilds_prompt_when_skill_files_change(self, monkeypatch, tmp_path):
+        monkeypatch.setenv("HERMES_HOME", str(tmp_path))
+        first_skill = tmp_path / "skills" / "tools" / "first-skill"
+        first_skill.mkdir(parents=True)
+        (first_skill / "SKILL.md").write_text(
+            "---\nname: first-skill\ndescription: First skill\n---\n"
+        )
+
+        first = build_skills_system_prompt()
+        assert "first-skill" in first
+        assert "second-skill" not in first
+
+        second_skill = tmp_path / "skills" / "tools" / "second-skill"
+        second_skill.mkdir(parents=True)
+        (second_skill / "SKILL.md").write_text(
+            "---\nname: second-skill\ndescription: Second skill\n---\n"
+        )
+
+        second = build_skills_system_prompt()
+        assert "first-skill" in second
+        assert "second-skill" in second
+
     def test_includes_setup_needed_skills(self, monkeypatch, tmp_path):
         monkeypatch.setenv("HERMES_HOME", str(tmp_path))
         monkeypatch.delenv("MISSING_API_KEY_XYZ", raising=False)
@@ -1088,4 +1110,3 @@ def test_guidance_is_string(self):
 # =========================================================================
 
 
-