diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 179eec9daf9..b48a4514921 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -455,22 +455,6 @@
     URI with ``mode=ro&uri=true``.
     For details see
     https://docs.galaxyproject.org/en/master/admin/tool_source_storage.html
-    A ``read_only`` store is trusted at boot whenever its persisted
-    index loads under the current index schema: it is published
-    together with the tools it indexes (the CVMFS model), so a
-    schema-valid index is authoritative by construction and no
-    per-tool coverage scan runs against it.
-    An entry may also declare a freshness probe via ``freshness``.
-    ``freshness: cvmfs`` reads the CernVM-FS repository revision (one
-    extended-attribute syscall) from ``freshness_path``, defaulting to
-    the store's SQLite file location; combined with
-    ``watch_tool_source_stores`` it lets Galaxy detect and reload a
-    newly published repository revision at runtime. ``freshness:
-    tool_confs`` hashes the local tool conf files plus tool_dir
-    directory mtimes and is compared at boot against the value the
-    populator stamped — the right probe for a writable store populated
-    on the same host; the default
-    (``tool_source_database_connection``) store always uses it.
 :Default: ``None``
 :Type: map
 
@@ -501,35 +485,6 @@
 :Type: int
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``watch_tool_source_stores``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Poll the freshness probes of read-only tool source stores and
-    reload the lazy toolbox index when a store's token changes (for
-    example, a new CVMFS repository revision was published).
-    Filesystem event watchers do not fire on CVMFS, so polling is the
-    only reliable signal; each poll costs one extended-attribute read
-    per watched store. Only meaningful with ``use_lazy_toolbox`` and a
-    ``tool_source_stores`` entry declaring a freshness probe. The
-    admin toolbox-reload API remains available as a manual trigger.
-:Default: ``false``
-:Type: bool
-
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``tool_source_store_watch_interval``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Seconds between freshness polls when ``watch_tool_source_stores``
-    is enabled. CVMFS clients only refresh their catalogs every few
-    minutes, so sub-minute polling buys nothing.
-:Default: ``60.0``
-:Type: float
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_dependency_dir``
 ~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/_galaxy_config_schema_attributes.py b/lib/galaxy/config/_galaxy_config_schema_attributes.py
index 5ca504b0fc6..110c3c9e662 100644
--- a/lib/galaxy/config/_galaxy_config_schema_attributes.py
+++ b/lib/galaxy/config/_galaxy_config_schema_attributes.py
@@ -41,8 +41,6 @@ class GalaxyAppConfigurationAttributes:
     tool_source_stores: Any
     use_lazy_toolbox: bool
     lazy_toolbox_cache_size: int
-    watch_tool_source_stores: bool
-    tool_source_store_watch_interval: float
     tool_dependency_dir: str | None
     dependency_resolvers_config_file: str
     conda_prefix: str | None
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index cdae74de11f..87fd65a4459 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -611,22 +611,6 @@ galaxy:
   # with ``mode=ro&uri=true``.
   # For details see
   # https://docs.galaxyproject.org/en/master/admin/tool_source_storage.html
-  # A ``read_only`` store is trusted at boot whenever its persisted
-  # index loads under the current index schema: it is published together
-  # with the tools it indexes (the CVMFS model), so a schema-valid index
-  # is authoritative by construction and no per-tool coverage scan runs
-  # against it.
-  # An entry may also declare a freshness probe via ``freshness``.
-  # ``freshness: cvmfs`` reads the CernVM-FS repository revision (one
-  # extended-attribute syscall) from ``freshness_path``, defaulting to
-  # the store's SQLite file location; combined with
-  # ``watch_tool_source_stores`` it lets Galaxy detect and reload a
-  # newly published repository revision at runtime. ``freshness:
-  # tool_confs`` hashes the local tool conf files plus tool_dir
-  # directory mtimes and is compared at boot against the value the
-  # populator stamped — the right probe for a writable store populated
-  # on the same host; the default (``tool_source_database_connection``)
-  # store always uses it.
   #tool_source_stores: null
 
   # When true, use the LazyToolBox which loads tools on demand from the
@@ -641,21 +625,6 @@ galaxy:
   # parsing cost for popular tools at the expense of memory.
   #lazy_toolbox_cache_size: 500
 
-  # Poll the freshness probes of read-only tool source stores and reload
-  # the lazy toolbox index when a store's token changes (for example, a
-  # new CVMFS repository revision was published). Filesystem event
-  # watchers do not fire on CVMFS, so polling is the only reliable
-  # signal; each poll costs one extended-attribute read per watched
-  # store. Only meaningful with ``use_lazy_toolbox`` and a
-  # ``tool_source_stores`` entry declaring a freshness probe. The admin
-  # toolbox-reload API remains available as a manual trigger.
-  #watch_tool_source_stores: false
-
-  # Seconds between freshness polls when ``watch_tool_source_stores`` is
-  # enabled. CVMFS clients only refresh their catalogs every few
-  # minutes, so sub-minute polling buys nothing.
-  #tool_source_store_watch_interval: 60.0
-
   # Various dependency resolver configuration parameters will have
   # defaults set relative to this path, such as the default conda
   # prefix, default Galaxy packages path, legacy tool shed dependencies
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 8323249e62a..016c39ee06b 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -357,24 +357,6 @@ mapping:
           For details see
           https://docs.galaxyproject.org/en/master/admin/tool_source_storage.html
 
-          A ``read_only`` store is trusted at boot whenever its persisted
-          index loads under the current index schema: it is published
-          together with the tools it indexes (the CVMFS model), so a
-          schema-valid index is authoritative by construction and no
-          per-tool coverage scan runs against it.
-
-          An entry may also declare a freshness probe via ``freshness``.
-          ``freshness: cvmfs`` reads the CernVM-FS repository revision (one
-          extended-attribute syscall) from ``freshness_path``, defaulting
-          to the store's SQLite file location; combined with
-          ``watch_tool_source_stores`` it lets Galaxy detect and reload a
-          newly published repository revision at runtime.
-          ``freshness: tool_confs`` hashes the local tool conf files plus
-          tool_dir directory mtimes and is compared at boot against the
-          value the populator stamped — the right probe for a writable
-          store populated on the same host; the default
-          (``tool_source_database_connection``) store always uses it.
-
       use_lazy_toolbox:
         type: bool
         required: false
@@ -394,29 +376,6 @@ mapping:
           in its in-memory LRU cache. Larger values reduce repeat parsing cost
           for popular tools at the expense of memory.
 
-      watch_tool_source_stores:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          Poll the freshness probes of read-only tool source stores and
-          reload the lazy toolbox index when a store's token changes (for
-          example, a new CVMFS repository revision was published).
-          Filesystem event watchers do not fire on CVMFS, so polling is the
-          only reliable signal; each poll costs one extended-attribute read
-          per watched store. Only meaningful with ``use_lazy_toolbox`` and
-          a ``tool_source_stores`` entry declaring a freshness probe. The
-          admin toolbox-reload API remains available as a manual trigger.
-
-      tool_source_store_watch_interval:
-        type: float
-        default: 60.0
-        required: false
-        desc: |
-          Seconds between freshness polls when ``watch_tool_source_stores``
-          is enabled. CVMFS clients only refresh their catalogs every few
-          minutes, so sub-minute polling buys nothing.
-
       tool_dependency_dir:
         type: str
         default: dependencies
diff --git a/lib/galaxy/queue_worker/__init__.py b/lib/galaxy/queue_worker/__init__.py
index 74ef479a7da..a998c012f00 100644
--- a/lib/galaxy/queue_worker/__init__.py
+++ b/lib/galaxy/queue_worker/__init__.py
@@ -296,7 +296,6 @@ def _get_new_toolbox(app: "UniverseApplication", save_integrated_tool_panel: boo
     tool_configs = app.config.tool_configs
 
     with app._toolbox_lock:
-        old_toolbox = app._toolbox
         new_toolbox: ToolBox
         if getattr(app.config, "use_lazy_toolbox", False) and getattr(app, "tool_source_store", None) is not None:
             new_toolbox = LazyToolBox(
@@ -321,15 +320,6 @@ def _get_new_toolbox(app: "UniverseApplication", save_integrated_tool_panel: boo
         for tool in new_toolbox.data_manager_tools.values():
             new_toolbox.register_tool(tool)
         app._toolbox = new_toolbox
-        # Retire the superseded box's background store watcher. In lazy mode
-        # each toolbox spawns a ToolSourceStoreWatcher daemon bound to itself;
-        # without this every reload leaks a polling thread that keeps grabbing
-        # app._toolbox_lock and disposing the shared store's engines on each
-        # republish. Only the watcher is stopped — in-flight reads on other
-        # threads still work, and the shared app.tool_source_store stays open.
-        # Eager ToolBoxes have no watcher, so guard on the lazy type.
-        if isinstance(old_toolbox, LazyToolBox) and old_toolbox is not new_toolbox:
-            old_toolbox.stop_watcher()
 
 
 def reload_data_managers(app, **kwargs):
diff --git a/lib/galaxy/tools/lazy_toolbox.py b/lib/galaxy/tools/lazy_toolbox.py
index 1bb0e812b3e..3074228d951 100644
--- a/lib/galaxy/tools/lazy_toolbox.py
+++ b/lib/galaxy/tools/lazy_toolbox.py
@@ -50,12 +50,10 @@ from galaxy.tools.source_store.index import (
     ToolPanelItem,
 )
 from galaxy.tools.source_store.populator import (
-    build_whoosh_for_store,
     conf_to_store_map,
     populate_for_paths,
     populate_store_inline,
 )
-from galaxy.tools.source_store.watcher import ToolSourceStoreWatcher
 from galaxy.util import listify
 from galaxy.util.tool_version import remove_version_from_guid
 from . import (
@@ -503,7 +501,6 @@ class LazyToolBox(ToolBox):
         # only the guid landed in the panel. Filled after the eager walk
         # via ``_rebuild_shed_short_id_map``.
         self._shed_short_id_to_guids: dict[str, set[str]] = {}
-        self._store_watcher: ToolSourceStoreWatcher | None = None
         # Identity-keyed cache of every indexed ``source_path`` — see
         # ``_index_source_paths``. Set before ``super().__init__`` because
         # the eager walk consults it through ``_tool_file_on_disk``.
@@ -538,59 +535,6 @@ class LazyToolBox(ToolBox):
             self._tools_loaded_from_store,
         )
 
-        self._start_store_watcher()
-
-    def _start_store_watcher(self) -> None:
-        """Poll externally-published stores for freshness-token changes.
-
-        Only read-only members with a probe are watched: writable stores
-        change through this process's own populate paths, which broadcast
-        their own reloads, and CVMFS (the read-only publishing model)
-        delivers no filesystem events to react to — polling one
-        extended-attribute read per store per tick is the whole cost.
-        """
-        if not self.app.config.watch_tool_source_stores:
-            return
-        if not isinstance(self._store, CompositeToolSourceStore):
-            log.info("watch_tool_source_stores is enabled but no named tool source stores are configured")
-            return
-        members = [(n, m) for n, m in self._store.members if m.read_only and m.has_freshness_probe]
-        if not members:
-            log.info("watch_tool_source_stores is enabled but no read-only store declares a freshness probe")
-            return
-        self._store_watcher = ToolSourceStoreWatcher(
-            members=members,
-            interval=self.app.config.tool_source_store_watch_interval,
-            on_change=self._on_store_freshness_change,
-        )
-        self._store_watcher.start()
-        log.info(
-            "Watching tool source store(s) %s for freshness changes every %gs",
-            sorted(n for n, _ in members),
-            self.app.config.tool_source_store_watch_interval,
-        )
-
-    def _on_store_freshness_change(self, changed_names: list[str]) -> None:
-        """A watched store was republished: reload index state and search.
-
-        ``invalidate_index_cache`` handles the reload dance (it also
-        disposes read-only members' engines — see there). The whoosh
-        rebuild runs here rather than in the reload path because only a
-        republished store can grow the corpus without a local populate;
-        its corpus-signature check makes re-runs no-ops, and concurrent
-        rebuilds from peer processes degrade to one winner (whoosh lock,
-        errors swallowed and logged by ``build_whoosh_for_store``).
-        """
-        self.invalidate_index_cache()
-        if not isinstance(self._store, CompositeToolSourceStore):
-            return
-        for name, member in self._store.members:
-            if name not in changed_names:
-                continue
-            index = member.load_index()
-            if index is not None:
-                build_whoosh_for_store(self.app.config, name, index)
-
     def _init_tools_from_configs(self, config_filenames: list[str]) -> None:
         """Load the persistent ``ToolIndex`` before delegating to the eager walk.
 
@@ -1792,18 +1736,6 @@ class LazyToolBox(ToolBox):
             if entry and entry.hidden:
                 tool.hidden = True
 
-    def stop_watcher(self) -> None:
-        """Stop the background store-freshness watcher, if one is running.
-
-        The reload path uses this to retire a superseded toolbox's watcher
-        thread without the class-level ``ToolLineage.reset()`` and index/store
-        teardown of ``close()`` — the replacement box is already live and the
-        shared ``tool_source_store`` must stay open. Idempotent.
-        """
-        if self._store_watcher is not None:
-            self._store_watcher.shutdown()
-            self._store_watcher = None
-
     def close(self) -> None:
         """Drop in-memory state at app shutdown.
 
@@ -1813,7 +1745,6 @@ class LazyToolBox(ToolBox):
         ``tool_source_store`` before the next boot wires up a fresh
         toolbox. Idempotent; safe to call more than once.
         """
-        self.stop_watcher()
         with self._cache_lock:
             self._tool_object_cache.clear()
         self._tool_index = None
diff --git a/lib/galaxy/tools/source_store/factory.py b/lib/galaxy/tools/source_store/factory.py
index 411b906ea9f..f2043577039 100644
--- a/lib/galaxy/tools/source_store/factory.py
+++ b/lib/galaxy/tools/source_store/factory.py
@@ -3,12 +3,9 @@
 import logging
 from typing import TYPE_CHECKING
 
-from sqlalchemy.engine import make_url
-
 from galaxy.tool_util.toolbox.parser import get_toolbox_parser
 from .composite import CompositeToolSourceStore
 from .freshness import (
-    cvmfs_probe,
     FreshnessProbe,
     tool_confs_probe,
 )
@@ -39,19 +36,6 @@ def _build_default_store(
     return SqlAlchemyToolSourceStore(url=url, read_only=False, freshness_probe=tool_confs_probe(config))
 
 
-def _sqlite_database_path(url: str) -> str | None:
-    """On-disk file behind a sqlite URL, or None for other backends."""
-    parsed = make_url(url)
-    if parsed.drivername.split("+")[0] != "sqlite":
-        return None
-    database = parsed.database
-    if not database or database == ":memory:":
-        return None
-    if database.startswith("file:"):
-        database = database[len("file:") :].split("?", 1)[0]
-    return database or None
-
-
 def _build_freshness_probe(
     name: str,
     spec: dict,
@@ -62,15 +46,8 @@ def _build_freshness_probe(
         return None
     if freshness == "tool_confs":
         return tool_confs_probe(config)
-    if freshness == "cvmfs":
-        probe_path = spec.get("freshness_path") or _sqlite_database_path(spec["url"])
-        if not probe_path:
-            raise ConfigurationError(
-                f"tool_source_stores[{name!r}] uses freshness: cvmfs with a non-file url; set freshness_path"
-            )
-        return cvmfs_probe(probe_path)
     raise ConfigurationError(
-        f"tool_source_stores[{name!r}] freshness must be 'cvmfs', 'tool_confs', or 'none' (got {freshness!r})"
+        f"tool_source_stores[{name!r}] freshness must be 'tool_confs' or 'none' (got {freshness!r})"
     )
 
 
@@ -82,7 +59,7 @@ def build_named_store(
     """Build a single named store from a ``tool_source_stores`` entry.
 
     ``spec`` is the dict from galaxy.yml - a SQLAlchemy ``url`` plus
-    optional ``read_only``, ``freshness``, and ``freshness_path`` keys.
+    optional ``read_only`` and ``freshness`` keys.
     Named stores get no probe unless one is declared: a store populated on
     a different host (the CVMFS publishing model) would never match a
     locally-computed conf hash, so ``tool_confs`` cannot be the default
diff --git a/lib/galaxy/tools/source_store/freshness.py b/lib/galaxy/tools/source_store/freshness.py
index 2e78a563500..62b6b6ee1e7 100644
--- a/lib/galaxy/tools/source_store/freshness.py
+++ b/lib/galaxy/tools/source_store/freshness.py
@@ -7,21 +7,18 @@ compares. A match certifies the store still covers the current tree, so
 boot skips the per-path coverage scan (and the populate it would trigger).
 A mismatch is always safe — it only falls back to scanning/populating.
 
-Two probe kinds exist:
+The built-in probe is ``tool_confs``: md5 over the tool and data-manager
+conf file contents, plus the (recursive) directory mtimes of any
+``tool_dir`` entries they declare. This captures tool
+additions/removals/renames — the same class of drift the coverage scan
+detects — without touching individual tool files. In-place edits to a
+tool's XML are invisible to both, by design: content changes are the
+incremental populate's job (raw-file md5), not the coverage check's.
+Wired to the default (writable) store automatically.
 
-- ``tool_confs``: md5 over the tool and data-manager conf file contents,
-  plus the (recursive) directory mtimes of any ``tool_dir`` entries they
-  declare. This captures tool additions/removals/renames — the same class
-  of drift the coverage scan detects — without touching individual tool
-  files. In-place edits to a tool's XML are invisible to both, by design:
-  content changes are the incremental populate's job (raw-file md5), not
-  the coverage check's. Wired to the default (writable) store
-  automatically.
-- ``cvmfs``: the CernVM-FS repository revision, read from the
-  ``user.revision`` extended attribute the CVMFS client exposes on the
-  mount point. One syscall covers every file in the repository. For a
-  store whose sqlite bundle is published in the same CVMFS transaction as
-  the tools it indexes, a matching revision is a hard consistency proof.
+Read-only stores need no probe for boot freshness — they are trusted as
+published (see ``SqlAlchemyToolSourceStore.index_is_fresh``); a probe on
+such a store only feeds the watcher's change detection.
 """
 
 import hashlib
@@ -99,38 +96,3 @@ def tool_confs_token(config: "GalaxyAppConfiguration") -> str:
 
 def tool_confs_probe(config: "GalaxyAppConfiguration") -> FreshnessProbe:
     return lambda: tool_confs_token(config)
-
-
-def _os_getxattr(path: str, attribute: str) -> bytes:
-    # ``os.getxattr`` only exists on Linux; CVMFS deployments are Linux.
-    getxattr = getattr(os, "getxattr", None)
-    if getxattr is None:
-        raise FreshnessProbeError("extended attributes are not supported on this platform")
-    return getxattr(path, attribute)
-
-
-def cvmfs_revision_token(path: str, _getxattr: Callable[[str, str], bytes] = _os_getxattr) -> str:
-    """CVMFS repository revision token for the repository containing ``path``.
-
-    The CVMFS client exposes repository metadata as extended attributes on
-    the mount point, so ascend from ``path`` until ``user.revision``
-    answers. Raises :class:`FreshnessProbeError` when no ancestor exposes
-    it — ``path`` isn't on CVMFS, or the repository isn't mounted (in
-    which case its tools are unreadable anyway, and "not fresh" is the
-    right verdict).
-    """
-    probe_path = os.path.abspath(path)
-    while True:
-        try:
-            revision = _getxattr(probe_path, "user.revision")
-        except OSError:
-            parent = os.path.dirname(probe_path)
-            if parent == probe_path:
-                raise FreshnessProbeError(f"no CVMFS revision xattr found on any ancestor of {path}")
-            probe_path = parent
-            continue
-        return f"cvmfs:{os.path.basename(probe_path)}:{revision.decode()}"
-
-
-def cvmfs_probe(path: str) -> FreshnessProbe:
-    return lambda: cvmfs_revision_token(path)
diff --git a/lib/galaxy/tools/source_store/watcher.py b/lib/galaxy/tools/source_store/watcher.py
index b92373f9070..dc1405c1b52 100644
--- a/lib/galaxy/tools/source_store/watcher.py
+++ b/lib/galaxy/tools/source_store/watcher.py
@@ -4,8 +4,7 @@ A store published outside this Galaxy process — the CVMFS model, where a
 publisher repopulates the sqlite bundle in the same transaction that ships
 new tools — changes without any local filesystem event (inotify does not
 fire on CVMFS). Polling each store's freshness probe is the only reliable
-signal, and it is cheap: one probe per store per tick, a single
-extended-attribute read for CVMFS stores.
+signal, and it is cheap: one probe per store per tick.
 
 The watcher itself is deliberately dumb: it detects token transitions and
 hands the changed store names to ``on_change``. Reload mechanics —
diff --git a/test/unit/app/queue_worker/test_reload_toolbox_watcher.py b/test/unit/app/queue_worker/test_reload_toolbox_watcher.py
deleted file mode 100644
index 0c87558f704..00000000000
--- a/test/unit/app/queue_worker/test_reload_toolbox_watcher.py
+++ /dev/null
@@ -1,68 +0,0 @@
-import threading
-from types import SimpleNamespace
-from unittest.mock import MagicMock
-
-from galaxy import queue_worker
-from galaxy.queue_worker import _get_new_toolbox
-from galaxy.tools.lazy_toolbox import LazyToolBox
-
-
-class FakeWatcher:
-    def __init__(self):
-        self.stopped = False
-
-    def shutdown(self):
-        self.stopped = True
-
-
-def _fake_new_toolbox(*args, **kwargs):
-    box = SimpleNamespace(data_manager_tools={})
-    box.register_tool = lambda tool: None
-    return box
-
-
-def _fake_app(old_toolbox):
-    app = SimpleNamespace()
-    app._toolbox_lock = threading.RLock()
-    app._toolbox = old_toolbox
-    app.toolbox = old_toolbox
-    app.datatypes_registry = MagicMock()
-    app.tool_source_store = None
-    app.config = SimpleNamespace(
-        use_lazy_toolbox=False,
-        tool_configs=[],
-        tool_path="/tmp/tools",
-        lazy_toolbox_cache_size=500,
-    )
-    return app
-
-
-def _patch_builders(monkeypatch):
-    monkeypatch.setattr(queue_worker, "ToolBox", _fake_new_toolbox)
-    monkeypatch.setattr(queue_worker, "load_lib_tools", lambda toolbox: None)
-
-
-def test_replacement_stops_superseded_lazy_watcher(monkeypatch):
-    _patch_builders(monkeypatch)
-    old = LazyToolBox.__new__(LazyToolBox)
-    old.data_manager_tools = {}
-    watcher = FakeWatcher()
-    old._store_watcher = watcher  # type: ignore[assignment]
-    app = _fake_app(old)
-
-    _get_new_toolbox(app)
-
-    assert watcher.stopped is True
-    assert old._store_watcher is None
-    assert app._toolbox is not old
-
-
-def test_eager_old_toolbox_is_left_untouched(monkeypatch):
-    _patch_builders(monkeypatch)
-    old = SimpleNamespace(data_manager_tools={})
-    app = _fake_app(old)
-
-    _get_new_toolbox(app)
-
-    assert app._toolbox is not old
-    assert not hasattr(old, "_store_watcher")
diff --git a/test/unit/app/tools/source_store/test_freshness.py b/test/unit/app/tools/source_store/test_freshness.py
index c66f8879510..d991ddc4aca 100644
--- a/test/unit/app/tools/source_store/test_freshness.py
+++ b/test/unit/app/tools/source_store/test_freshness.py
@@ -2,11 +2,8 @@
 
 import logging
 
-import pytest
-
 from galaxy.tools.source_store.composite import CompositeToolSourceStore
 from galaxy.tools.source_store.freshness import (
-    cvmfs_revision_token,
     FreshnessProbeError,
     tool_confs_token,
 )
@@ -53,24 +50,6 @@ def test_tool_confs_token_sees_tool_dir_membership_changes(tmp_path):
     assert tool_confs_token(cfg) != after_top_level
 
 
-def test_cvmfs_revision_token_ascends_to_the_mount_root():
-    def fake_getxattr(path, attribute):
-        if path == "/cvmfs/main.galaxyproject.org" and attribute == "user.revision":
-            return b"1042"
-        raise OSError(61, "no attribute")
-
-    token = cvmfs_revision_token("/cvmfs/main.galaxyproject.org/galaxy/store.sqlite", _getxattr=fake_getxattr)
-    assert token == "cvmfs:main.galaxyproject.org:1042"
-
-
-def test_cvmfs_revision_token_raises_off_cvmfs():
-    def fake_getxattr(path, attribute):
-        raise OSError(61, "no attribute")
-
-    with pytest.raises(FreshnessProbeError):
-        cvmfs_revision_token("/plain/local/path", _getxattr=fake_getxattr)
-
-
 def test_index_is_fresh_tracks_probe(tmp_path):
     current = {"token": "confs:a"}
     store = SqlAlchemyToolSourceStore(url=f"sqlite:///{tmp_path}/a.sqlite", freshness_probe=lambda: current["token"])
@@ -92,7 +71,7 @@ def test_index_is_fresh_false_when_probe_fails(tmp_path):
         raise FreshnessProbeError("repo not mounted")
 
     store = SqlAlchemyToolSourceStore(url=f"sqlite:///{tmp_path}/a.sqlite", freshness_probe=broken_probe)
-    store.store_index(ToolIndex(freshness_token="cvmfs:r:1"))
+    store.store_index(ToolIndex(freshness_token="bundle:1"))
     assert store.index_is_fresh() is False
 
 
@@ -102,14 +81,14 @@ def _stamped_store(path, token, probe_token, read_only=False):
 
 
 def test_composite_fresh_when_all_members_fresh(tmp_path):
-    ro = _stamped_store(tmp_path / "ro.sqlite", "cvmfs:r:1", "cvmfs:r:1", read_only=True)
+    ro = _stamped_store(tmp_path / "ro.sqlite", "bundle:1", "bundle:1", read_only=True)
     rw = _stamped_store(tmp_path / "rw.sqlite", "confs:x", "confs:x")
     composite = CompositeToolSourceStore(members=[("ro", ro), ("rw", rw)], default="rw")
     assert composite.index_is_fresh() is True
 
 
 def test_composite_stale_writable_member_wins(tmp_path):
-    ro = _stamped_store(tmp_path / "ro.sqlite", "cvmfs:r:1", "cvmfs:r:1", read_only=True)
+    ro = _stamped_store(tmp_path / "ro.sqlite", "bundle:1", "bundle:1", read_only=True)
     rw = _stamped_store(tmp_path / "rw.sqlite", "confs:x", "confs:y")
     composite = CompositeToolSourceStore(members=[("ro", ro), ("rw", rw)], default="rw")
     assert composite.index_is_fresh() is False
@@ -118,14 +97,14 @@ def test_composite_stale_writable_member_wins(tmp_path):
 def test_read_only_store_trusts_schema_valid_index_over_probe(tmp_path):
     # Stamped token and probe value disagree, but a read-only store is
     # trusted whenever its index loads — the probe only feeds the watcher.
-    ro = _stamped_store(tmp_path / "ro.sqlite", "cvmfs:r:1", "cvmfs:r:2", read_only=True)
+    ro = _stamped_store(tmp_path / "ro.sqlite", "bundle:1", "bundle:2", read_only=True)
     assert ro.index_is_fresh() is True
 
 
 def test_read_only_store_without_index_is_not_fresh(tmp_path):
     SqlAlchemyToolSourceStore(url=f"sqlite:///{tmp_path}/ro.sqlite")
     ro = SqlAlchemyToolSourceStore(
-        url=f"sqlite:///{tmp_path}/ro.sqlite", read_only=True, freshness_probe=lambda: "cvmfs:r:1"
+        url=f"sqlite:///{tmp_path}/ro.sqlite", read_only=True, freshness_probe=lambda: "bundle:1"
     )
     assert ro.index_is_fresh() is False
 
@@ -141,7 +120,7 @@ def test_composite_read_only_member_without_index_warns_but_stays_fresh(tmp_path
 
 
 def test_composite_member_without_probe_downgrades_to_none(tmp_path):
-    ro = _stamped_store(tmp_path / "ro.sqlite", "cvmfs:r:1", "cvmfs:r:1", read_only=True)
+    ro = _stamped_store(tmp_path / "ro.sqlite", "bundle:1", "bundle:1", read_only=True)
     rw = SqlAlchemyToolSourceStore(url=f"sqlite:///{tmp_path}/rw.sqlite")
     composite = CompositeToolSourceStore(members=[("ro", ro), ("rw", rw)], default="rw")
     assert composite.index_is_fresh() is None