diff --git a/tests/tools/test_tool_manifest_cache.py b/tests/tools/test_tool_manifest_cache.py
index 6ddd118bb44..75bb760de88 100644
--- a/tests/tools/test_tool_manifest_cache.py
+++ b/tests/tools/test_tool_manifest_cache.py
@@ -64,6 +64,19 @@ class TestManifestCache:
         assert loaded is not None
         assert loaded == ["tools.alpha", "tools.beta"]
 
+    def test_cache_miss_when_tools_dir_differs(self, tool_dir, cache_path, tmp_path):
+        """A manifest built for one checkout must not serve another checkout."""
+        module = _load_registry_module()
+        module._save_manifest_cache(cache_path, tools_dir=tool_dir, module_names=["tools.alpha", "tools.beta"])
+        other = tmp_path / "other" / "tools"
+        other.mkdir(parents=True)
+        # Mirror the exact files/mtimes so only tools_dir differs.
+        import shutil
+        for p in tool_dir.glob("*.py"):
+            dest = other / p.name
+            shutil.copy2(p, dest)
+        assert module._load_manifest_cache(cache_path, tools_dir=other) is None
+
     def test_cache_miss_when_file_missing(self, tool_dir, cache_path):
         module = _load_registry_module()
         assert module._load_manifest_cache(cache_path, tools_dir=tool_dir) is None
diff --git a/tools/registry.py b/tools/registry.py
index 8eb18bc6e00..b2f09fb1584 100644
--- a/tools/registry.py
+++ b/tools/registry.py
@@ -98,7 +98,11 @@ def _save_manifest_cache(cache_path: Path, tools_dir: Path, module_names: List[s
             "module_names": module_names,
             "mtimes": _collect_tool_file_mtimes(tools_dir),
         }
-        cache_path.write_text(json.dumps(payload, indent=2, sort_keys=True) + "\n", encoding="utf-8")
+        # Atomic replace so a concurrent reader (gateway + CLI + cron can all
+        # cold-start at once) never sees a torn/partial JSON file.
+        tmp_path = cache_path.with_name(cache_path.name + f".tmp{os.getpid()}")
+        tmp_path.write_text(json.dumps(payload, indent=2, sort_keys=True) + "\n", encoding="utf-8")
+        os.replace(tmp_path, cache_path)
     except Exception:
         logger.debug("Failed to save tool manifest cache", exc_info=True)
 
@@ -113,6 +117,12 @@ def _load_manifest_cache(cache_path: Path, tools_dir: Path) -> Optional[List[str
         return None
     if not isinstance(data, dict) or data.get("version") != 1:
         return None
+    # A shared HERMES_HOME can be used by several checkouts (main clone +
+    # worktrees). The manifest is only valid for the tools dir it was built
+    # from — otherwise identical mtimes across copies could serve a stale
+    # module list from a different tree.
+    if data.get("tools_dir") != str(tools_dir):
+        return None
     cached_mtimes = data.get("mtimes", {})
     current_mtimes = _collect_tool_file_mtimes(tools_dir)
     if cached_mtimes != current_mtimes: