diff --git a/docs/dev-notes/linked-file-features.md b/docs/dev-notes/linked-file-features.md
index 2e51a0a823..445b33989c 100644
--- a/docs/dev-notes/linked-file-features.md
+++ b/docs/dev-notes/linked-file-features.md
@@ -295,6 +295,26 @@ stay compatible.
 - Debugging note: merged cut groups carry member guids as CSS *classes*, not as the
   `ifcopenshell:guid` attribute — inspect both when checking cut output.
 
+## Deferred refactors (deliberate)
+
+- **Upstream `exclude=` on `filter_elements`** — the include−exclude set difference
+  is hand-rolled twice (links, drawings) because the selector grammar has no
+  difference operator and `parent` negation is broken by design (its `!=`/regex
+  paths also match GlobalIds, so negation strips everything that has a parent).
+  The right home is an `exclude=` parameter on
+  `ifcopenshell.util.selector.filter_elements`, documented in
+  `selector_syntax.rst` together with the `parent`-negation limitation. Deferred
+  to a separate ifcopenshell-python PR (different review audience; would widen
+  this PR mid-review). Once it lands, both Bonsai call sites collapse.
+- **Core/tool ceremony skipped** — the new `tool.Project` methods have no
+  `core/tool.py` interface declarations and no `bonsai/core` orchestration
+  functions, matching the pre-existing linked-model code (which bypasses the
+  core layer wholesale; `LoadLinkedProject` is flagged "prototyping" upstream).
+  Interfaces nobody calls through wouldn't add testability — the pure helpers
+  (`encode_link_filter`/`decode_link_filter`, `get_link_cache_paths`) are
+  covered directly in `test/tool/test_project.py` instead. Revisit if the
+  linked-model subsystem is ever promoted out of prototype status.
+
 ## Review round 1 (PR #8242, falken10vdl) — decisions
 
 - **Path-form mismatch → duplicate documents (confirmed bug, fixed).**
diff --git a/src/bonsai/bonsai/bim/module/project/__init__.py b/src/bonsai/bonsai/bim/module/project/__init__.py
index f59b4b4d5b..b32c3b16db 100644
--- a/src/bonsai/bonsai/bim/module/project/__init__.py
+++ b/src/bonsai/bonsai/bim/module/project/__init__.py
@@ -112,7 +112,14 @@ addon_keymaps = []
 
 @bpy.app.handlers.persistent
 def _autosave_link_transforms(scene, depsgraph):
-    """Persist link transformations whenever an editing link's handle is moved."""
+    """Persist link transformations whenever an editing link's handle is moved.
+
+    Deliberate exemption from the transaction rule in
+    docs/guides/development/undo_system.rst: a handler cannot run inside
+    execute_ifc_operator, so this IFC write is not undo-tracked. It stays
+    consistent anyway because undoing the move fires another depsgraph
+    update, which re-saves the reverted matrix.
+    """
     import bonsai.tool as tool
 
     props = tool.Project.get_project_props()
diff --git a/src/bonsai/test/tool/test_project.py b/src/bonsai/test/tool/test_project.py
index 2520ab12d0..7bcbe07055 100644
--- a/src/bonsai/test/tool/test_project.py
+++ b/src/bonsai/test/tool/test_project.py
@@ -501,3 +501,67 @@ class TestGettingLinkedElementGeomSlice:
         obj = cast(bpy.types.Object, obj)
         slice_ = subject.Link.get_linked_element_geom_slice(obj, "aaa")
         assert range(15)[slice_] == range(5)
+
+
+class TestEncodeDecodeLinkFilter:
+    def test_plain_include_round_trip(self):
+        assert subject.encode_link_filter("IfcWall", "") == "IfcWall"
+        assert subject.decode_link_filter("IfcWall") == ("IfcWall", "", False)
+
+    def test_empty_filter_encodes_to_none(self):
+        assert subject.encode_link_filter("", "") is None
+        assert subject.decode_link_filter(None) == ("", "", False)
+        assert subject.decode_link_filter("") == ("", "", False)
+
+    def test_exclude_promotes_to_json(self):
+        encoded = subject.encode_link_filter('IfcElement, group="X"', 'IfcSlab, parent="Y"')
+        assert encoded.startswith("{")
+        assert subject.decode_link_filter(encoded) == ('IfcElement, group="X"', 'IfcSlab, parent="Y"', False)
+
+    def test_loaded_promotes_to_json(self):
+        encoded = subject.encode_link_filter("IfcWall", "", loaded=True)
+        assert encoded.startswith("{")
+        assert subject.decode_link_filter(encoded) == ("IfcWall", "", True)
+
+    def test_loaded_without_filter(self):
+        encoded = subject.encode_link_filter("", "", loaded=True)
+        assert subject.decode_link_filter(encoded) == ("", "", True)
+
+    def test_legacy_non_json_decodes_as_include(self):
+        legacy = 'IfcElement, location="House - Type B"'
+        assert subject.decode_link_filter(legacy) == (legacy, "", False)
+
+    def test_malformed_json_decodes_as_include(self):
+        assert subject.decode_link_filter("{not json") == ("{not json", "", False)
+
+
+class TestGetLinkCachePaths:
+    def test_empty_filter_keeps_legacy_names(self):
+        blend, json_ = subject.get_link_cache_paths("/x/File A.ifc", "")
+        assert blend.name == "File A.ifc.cache.blend"
+        assert json_.name == "File A.ifc.cache.json"
+
+    def test_include_only_hash_matches_pre_exclude_formula(self):
+        # Existing caches were keyed by md5(query)[:8]; they must stay valid.
+        import hashlib
+
+        blend, _ = subject.get_link_cache_paths("/x/File A.ifc", "IfcWall")
+        expected = hashlib.md5(b"IfcWall").hexdigest()[:8]
+        assert blend.name == f"File A.ifc.cache.{expected}.blend"
+
+    def test_blend_and_json_share_a_suffix(self):
+        blend, json_ = subject.get_link_cache_paths("/x/File A.ifc", "IfcWall", "IfcDoor")
+        assert blend.name.removesuffix("blend") == json_.name.removesuffix("json")
+
+    def test_same_include_different_exclude_do_not_collide(self):
+        # The reason the cache key hashes both strings: same-include links
+        # with different excludes must not serve each other's geometry.
+        a, _ = subject.get_link_cache_paths("/x/f.ifc", "IfcElement", "IfcSlab")
+        b, _ = subject.get_link_cache_paths("/x/f.ifc", "IfcElement", "IfcDoor")
+        c, _ = subject.get_link_cache_paths("/x/f.ifc", "IfcElement", "")
+        assert len({a.name, b.name, c.name}) == 3
+
+    def test_exclude_only_distinct_from_empty_filter(self):
+        a, _ = subject.get_link_cache_paths("/x/f.ifc", "", "IfcDoor")
+        b, _ = subject.get_link_cache_paths("/x/f.ifc", "", "")
+        assert a.name != b.name