diff --git a/hermes_cli/plugins_cmd_catalog.py b/hermes_cli/plugins_cmd_catalog.py
index a7ddbb4077..e904ee3191 100644
--- a/hermes_cli/plugins_cmd_catalog.py
+++ b/hermes_cli/plugins_cmd_catalog.py
@@ -359,6 +359,8 @@ def _carry_user_files(old: Path, new: Path, local: Optional[list[str]]) -> list[
     tree are carried while executable/declarative plugin surfaces remain revision-owned. If a
     user-owned path cannot be represented safely in the new tree (a layout clash, or a symlink in a
     git checkout's untracked/ignored set), fail before publication rather than silently dropping it.
+    Dirs in ``tools.plugin_guard.EXCLUDED_DIRS`` (``.venv/``, ``node_modules/``, tool caches) are
+    install artefacts: they are neither carried nor inspected, so links inside them never stop an update.
     Returns the carried paths (POSIX, relative to the tree) so a later scan block can name them.
     """
     from hermes_cli.plugins_cmd import PluginOperationError
@@ -371,9 +373,7 @@ def _carry_user_files(old: Path, new: Path, local: Optional[list[str]]) -> list[
     def _user_link(rel: Path) -> None:
         # Git-owned user state that is a symlink is refused, never followed: a link injected after the
         # installer's scan could point outside the plugin root past the guard (which skips links).
-        # Links under the guard's excluded dirs (node_modules/.bin shims, .venv/bin/python) are
-        # reproducible install artefacts, not user state.
-        if local is not None and not keep.isdisjoint((rel, *rel.parents)) and EXCLUDED_DIRS.isdisjoint(rel.parts):
+        if local is not None and not keep.isdisjoint((rel, *rel.parents)):
             linked.append(rel.as_posix())
 
     def _walk_error(exc: OSError) -> None:
@@ -388,8 +388,12 @@ def _carry_user_files(old: Path, new: Path, local: Optional[list[str]]) -> list[
         here = Path(dirpath)
         walk = []
         for name in dirnames:
-            # Without git, top-level revision-owned dirs are never carried: do not even walk them.
-            if _skip_preserve(name) or (local is None and here == old and name in _NO_GIT_REVISION_DIRS):
+            # The guard's excluded dirs (.venv, node_modules, tool caches) are reproducible install
+            # artefacts, not user state: never walk or carry them, so the fresh tree rebuilds them whole
+            # (a partial copy has no bin/python or .bin shims and suppresses `npm ci`). Without git,
+            # top-level revision-owned dirs are never carried either.
+            if (_skip_preserve(name) or name in EXCLUDED_DIRS
+                    or (local is None and here == old and name in _NO_GIT_REVISION_DIRS)):
                 continue
             if (here / name).is_symlink() or is_junction(here / name):
                 _user_link((here / name).relative_to(old))
diff --git a/tests/hermes_cli/test_plugins_cmd_catalog.py b/tests/hermes_cli/test_plugins_cmd_catalog.py
index 06c0a47b6a..9f5e360302 100644
--- a/tests/hermes_cli/test_plugins_cmd_catalog.py
+++ b/tests/hermes_cli/test_plugins_cmd_catalog.py
@@ -264,7 +264,7 @@ def test_update_of_a_subdir_install_keeps_files_the_user_created_or_edited(world
 def test_repin_keeps_a_wholly_ignored_data_dir_in_a_git_checkout(world):
     """A single ``!! data/`` status entry must preserve every file below that ignored directory."""
     repo = world["repo"]
-    (repo / ".gitignore").write_text("data/\n.venv/\n")
+    (repo / ".gitignore").write_text("data/\n.venv/\nnode_modules/\n")
     world["state"]["pin"] = _commit(repo, "ignore data")
     target = cat.install_catalog_entry(pc_cat.get_live_catalog_entry("cat-plugin"), force=False)[0]
     assert (target / ".git").exists()
@@ -274,6 +274,9 @@ def test_repin_keeps_a_wholly_ignored_data_dir_in_a_git_checkout(world):
     # An ignored venv always holds symlinks (bin/python); it is a reproducible artefact, not user state.
     (target / ".venv" / "bin").mkdir(parents=True)
     (target / ".venv" / "bin" / "python").symlink_to("/usr/bin/python3")
+    (target / ".venv" / "pyvenv.cfg").write_text("home = /usr/bin")
+    (target / "node_modules" / "x").mkdir(parents=True)
+    (target / "node_modules" / "x" / "index.js").write_text("module.exports = 1")
 
     (repo / "__init__.py").write_text("def register(ctx):\n    pass  # v3\n")
     world["state"]["pin"] = _commit(repo, "v3")
@@ -281,6 +284,8 @@ def test_repin_keeps_a_wholly_ignored_data_dir_in_a_git_checkout(world):
 
     assert _head(target) == world["state"]["pin"]
     assert (target / "data" / "db" / "index.db").read_text() == "user data"
+    # Excluded dependency dirs are not carried at all: a partial copy would be a broken install.
+    assert not (target / ".venv").exists() and not (target / "node_modules").exists()
 
     # A symlink in the ignored set is never followed into the update: it fails closed, naming the path,
     # and the live plugin stays at its current revision with its user data.