Bonsai: custom display names for links

Each link row draws an editable display_name (double-click to rename)
with the file path as placeholder while unset, so several links of the
same file can be told apart. The name persists in the same Description
JSON blob as the filter and loaded state (new name key, written at
save time and by reload_link), restores on project open, and plain
legacy strings still decode unchanged. Decode tests updated to the
four-tuple with a name round-trip case.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/dev-notes/linked-file-features.md

@@ -0,0 +1,400 @@
+<!-- This file was generated with the assistance of an AI coding tool. -->
+
+# Linked file features — queries, styles, transforms, and multi-linking for linked IFC models
+
+> **Living dev note** for the `Linked_File_Features` branch/PR. Read before working
+> on the feature; append decisions and findings as the PR is refined. This is *not* user
+> documentation — at merge it is removed or its durable parts promoted to code comments.
+> See [README.md](README.md) for the convention (introduced on the
+> `opening-template-on-type` branch; not yet on this branch's base).
+
+## Problem
+
+Linked IFC models (`bim.link_ifc`) had several gaps that made them hard to use as a
+"reference in other trades' models" workflow:
+
+- One shared `.ifc.cache.blend` per IFC file meant the **same file could not be linked
+  twice with different selector queries** — both links showed whichever query was cached
+  first in-session, and whichever was cached last after reopening (Blender reuses one
+  library datablock per path).
+- The selector query was not durably stored anywhere in the host IFC, so save → reopen
+  lost or cross-wired the filter; a scripted `bpy.ops.bim.reload_link()` also wiped it.
+- Linked geometry got **flat diffuse-only materials** — external `.blend` styles
+  (`IfcExternallyDefinedSurfaceStyle`) and per-layer materials (layerset slicing) that
+  the normal import applies were ignored.
+- Moving a linked model required an explicit enable-edit → move → save dance on the
+  active link only, with save/cancel buttons in the panel header.
+- The Explore tool's highlight broke (GPU type errors), drew at the link's *original*
+  location when the link had been moved, and `bim.append_inspected_linked_element`
+  placed appended elements at the original location too.
+
+## Key facts established
+
+- **Cache architecture**: `LoadLink.link_ifc` generates a Python script and runs a
+  background Blender subprocess that executes `bim.load_linked_project` and saves a
+  `.ifc.cache.blend`. The host session then *links* (not appends) the `IfcProject/...`
+  collection from that blend and instances it via an empty (the link "handle").
+  Georeferencing metadata lives in a sidecar `.cache.json`; extracted properties in
+  `.cache.sqlite` (whole file, query-independent — deliberately shared across queries).
+- **Blender reuses an in-session library per path.** Loading the same blend path twice
+  yields the same library/collection. This is what broke multi-query linking with a
+  shared cache filename, and why per-query *filenames* (not cache invalidation) are the
+  fix.
+- **Last-used operator properties** are reused on the next *interactive* invocation
+  (UI button), while scripted `bpy.ops` calls always start from defaults. LoadLink's
+  internal `self.query = link.query` fallback assignment was remembered by Blender and
+  leaked into the next button click (`operator_query='IfcWindow'` for the door link).
+  Any `is_property_set()`-based logic is corrupted the same way. Fix: `SKIP_SAVE` on
+  volatile props. **A GUI-only bug like this is invisible to scripted repro** — both
+  headless and windowed `--python` test runs passed while the manual flow failed.
+- **`IfcDocumentReference`** per link: attribute index 1 (`Identification`) already
+  stores the link's 4×4 transformation (existing Bonsai convention). `Description`
+  (IFC4+; **absent in IFC2X3**) now stores the selector query. One
+  `IfcDocumentInformation` (Scope `LINKED_MODEL`) per file, one reference per link.
+- **Geometry iterator materials**: `material.instance_id()` is the STEP id of the
+  `IfcSurfaceStyle` — or of an `IfcMaterial` when the item has a material but no style,
+  hence the `is_a("IfcSurfaceStyle")` guard when resolving external styles.
+- **External styles**: `IfcExternallyDefinedSurfaceStyle.Location` (`.blend`, relative
+  paths resolve against the *linked* IFC, not the host) + `Identification` in
+  `data_block_type/name` form (e.g. `materials/Brick`), same convention as
+  `bim.activate_external_style`.
+- **Chunk pipeline dedups materials by RGBA color** (`np.unique` on a color array), so
+  style identity must ride along as an extra column to survive — added only for styles
+  that actually resolve to an external material, so plain colored styles dedupe exactly
+  as before.
+- **`slice_layerset_mesh` needs a local-space, per-element mesh** (bisect planes are in
+  object space), which the chunk path can't provide (world-space, many elements per
+  mesh) — hence routing multi-layer elements through the instanced path. Its
+  `dissolve_limit` produces **ngons**, which broke the Explore highlight's
+  triangles-from-`polygon.vertices` assumption downstream.
+- **ID properties round-trip as `IDPropertyArray`**, not plain lists (verified in
+  4.5.7: empty list → flat `IDPropertyArray`; nested lists → list of `IDPropertyArray`
+  items), and `GPUIndexBuf` rejects them — selection geometry must be converted to
+  plain tuples on read.
+- **`scene.ray_cast` returns the hit instance's world matrix** (link empty matrix
+  included). For instanced occurrence objects the object's own local matrix is *not*
+  identity, so resolving the instancing empty must compare against
+  `empty.matrix_world @ obj.matrix_world`, not the empty's matrix alone.
+- **Link matrix math**: the handle empty's matrix is `inv(L) @ T @ G` (L = host local
+  matrix from georef props, T = stored transformation, G = linked model's global
+  matrix from the cache json). The world-space displacement of a moved link is
+  therefore `inv(L) @ T @ L` — no json read needed (`calculate_link_delta_matrix`).
+- **Undo consistency of auto-saved moves**: Blender undo of a handle move fires another
+  depsgraph update, so the handler re-saves the reverted matrix — stored state stays
+  consistent without transactions (a handler can't open one).
+
+## Design
+
+### Per-query caches + query persistence (multi-linking)
+
+`tool.Project.get_link_cache_paths(filepath, query)` appends `.md5(query)[:8]` to the
+cache blend/json names; the empty query keeps the legacy un-suffixed names so existing
+caches stay valid. Every cache-path consumer goes through it — `link_ifc` build and
+invalidation, the subprocess json write, model-origin/georef indicator reads,
+`calculate_link_matrix`, `save_link_transformation`, and the per-link
+selectability/wireframe/visibility toggles (which match collections *by library
+filepath* and would otherwise affect every link of the file at once).
+
+The query persists on each link's `IfcDocumentReference.Description` (written by
+`LinkIfc` and `ReloadLink`); `load_linked_models_from_ifc` restores from it, with a
+legacy-JSON fallback that only applies when the file has a **single** link (with
+several links the shared JSON can't say which link it belonged to). IFC2X3 hosts have
+no `Description` — custom queries are not restorable there (accepted).
+
+`LoadLink`/`ReloadLink` volatile properties are `SKIP_SAVE` (see key facts). Cache
+clearing tolerates a missing blend (a reload with a brand-new query points at a
+not-yet-existing filename).
+
+### Include/Exclude filter pair
+
+The selector grammar's only cross-group combiner is `+` (union) and the `parent`
+facet cannot express "not under X" (its `!=`/regex paths also match by GlobalId, so
+negation removes everything with any parent), which makes set differences like
+"group members minus the slabs under aggregate X" structurally inexpressible in one
+query string. Links therefore carry an **Exclude** query beside the include —
+mirroring `EPset_Drawing`'s Include/Exclude pattern: final set = include (or the
+default set when empty) − exclude, applied in `LoadLinkedProject` and per link in
+`create_drawing`.
+
+- **Cache key**: `get_link_cache_paths` hashes `md5(query + "\0" + exclude)` when an
+  exclude exists; include-only filters keep the pre-exclude `md5(query)` so existing
+  caches stay valid; empty filter keeps legacy un-suffixed names. Keying on query
+  alone would let same-include/different-exclude links silently serve each other's
+  geometry.
+- **Persistence**: `encode_link_filter`/`decode_link_filter` — a plain include is
+  stored in `Description` as-is (backwards compatible); an exclude, a `loaded`
+  state or a custom display name promotes the value to
+  `{"include": …, "exclude": …, "loaded": …, "name": …}` JSON. Decode treats
+  non-JSON as a legacy include string. The display name (`Link.display_name`,
+  double-click the list row to rename; file path shows as placeholder while
+  unset) exists to tell apart several links of the same file.
+- Exclude applies on top of the **default** element set too, so
+  "everything except X" needs no explicit include.
+- UI labels are **Include**/**Exclude** (matching the drawing pattern), but the
+  property identifier stays `query` for script (`bpy.ops.bim.link_ifc(query=…)`)
+  and persistence compatibility.
+- Verified headless: `query=""`/`exclude="IfcDoor"` loads only the window;
+  same file with a different filter gets its own cache; both filters survive
+  save → reopen → reload.
+
+### Auto-load on open
+
+Links that were **loaded and visible** at IFC save time auto-load when the project
+is reopened. `ExportIFC` calls `tool.Project.update_linked_models_state()`, which
+rewrites each reference's `Description` with a `loaded` flag
+(`is_loaded and not is_hidden`); `load_linked_models_from_ifc` replays flagged
+links via `load_link` after restoring the list (missing files warn and skip so
+they can't break project open). The flag extends the same JSON blob as the
+exclude — plain legacy strings decode as no-autoload. Trade-off: project open
+pays the link-load cost up front (fast on cache hit; a missing cache rebuilds in
+a background Blender, same as clicking Load). Verified headless: loaded+visible
+auto-loads; unloaded and loaded-but-hidden links stay unloaded.
+
+### Long-term serialization target: STEP Part 21 Edition 3
+
+STEP p21e3 defines the standards-track version of this feature's persistence:
+`ANCHOR`/`REFERENCE` sections (clauses 9–10) let one file import entities from
+another via URI + fragment, and **anchor tags** (`{tagname: value}`) are the
+designated slot for out-of-schema metadata — a cleaner home than the
+`Description` JSON blob (see the review-round discussion). ifcopenshell does not
+implement these sections yet ([#668](https://github.com/IfcOpenShell/IfcOpenShell/issues/668),
+open, unassigned); if it ever does, the migration path is: link →
+`REFERENCE` to the linked file's project anchor, filter/transform/loaded
+metadata → anchor tags. Keeping the blob behind
+`encode_link_filter`/`decode_link_filter` makes that a two-function change.
+
+Two p21e3 design points this branch already conforms to:
+
+- **Identity**: p21e3 distinguishes volatile file-scoped entity numbers
+  (`#100` fragments) from durable anchors/UUIDs — the same lesson behind our
+  STEP-id collision fixes (GUID-based matching, `element.file` guards). Raw
+  STEP ids must never cross a file boundary; IFC GlobalIds map 1:1 onto
+  p21e3 UUID anchors.
+- **Transport** (clause A.4): exchange structures plus referenced resources
+  can ship as one ZIP archive with references resolving inside it. Our posix,
+  optionally relative `Location`s resolved via `resolve_uri` are exactly the
+  invariants a future "package project with links" export would need.
+
+Even full p21e3 support would not cover per-link transforms, filters, or load
+state — a `REFERENCE` imports entities, it does not place a model — so the
+app-level metadata remains; only its container would change.
+
+### External styles + layerset slicing in the linked loader
+
+`LoadLinkedProject.get_external_material(style_id)` resolves a style id → appended
+Blender material from the external `.blend`, cached two ways (per style id; per
+appended data-block, so styles sharing one material don't append duplicates). Appended
+materials get their stale `ifc_definition_id` cleared (the source `.blend` may have
+been authored in a Bonsai session; the id would be misread in the linked file *and*
+in the host once the cache links in). Applied in both loading paths — instanced
+occurrences directly, chunks via the style-id column.
+
+Multi-layer elements (`IfcMaterialLayerSetUsage`, >1 layer) route through the
+instanced path and get `slice_layerset_mesh`, which gained a pluggable
+`style_to_material` resolver (defaults to the old `tool.Ifc.get_object` for the normal
+import) — the linked resolver prefers the external material, falling back to a flat
+diffuse from the style's shading colour. Also fixed there: newly appended layer
+materials are registered in the dedup dict (two layers sharing one style used to
+append it twice).
+
+Trade-off: layered walls become individual instanced objects instead of chunk members;
+meshes shared between elements (same geometry id) bake the slice from the first
+element's layerset usage — same behaviour as the normal importer.
+
+### Reload Link dialog
+
+`bim.reload_link` now exposes File Path (+ browse button), Use Relative Path
+(defaulting to the stored path form), Use Cache (default off = old always-rebuild
+behaviour), the False Origin Mode project props, and Query. A file browser can't open
+from inside a props dialog, so the browse button runs `bim.select_link_filepath`
+(fileselect) which *reopens* the reload dialog with the chosen path, carrying the
+in-progress dialog state through the round trip (op props are baked at draw time).
+Path changes update `link.name`/`filepath` and, with a host IFC, the reference
+`Location` + document name — which is why `ReloadLink` became a `tool.Ifc.Operator`.
+Script calls without arguments preserve all stored link values via `is_property_set`.
+
+`bim.reload_all_links` (refresh button beside Link IFC in the panel header) reloads
+every *loaded* link via argument-less `reload_link` calls — each link's stored
+path/query/exclude replay and its cache rebuilds from disk. Unloaded links are left
+alone. Deliberately expensive: one background cache rebuild per link.
+
+### Per-row lock toggle + auto-saved transforms
+
+Link editing moved from the panel header into each list row as a lock/unlock icon:
+unlock (`bim.enable_editing_link`) frees the handle; **any movement is persisted
+immediately** by a `depsgraph_update_post` handler (lazy — ticks without transform
+updates cost ~nothing); lock (`bim.disable_editing_link`) saves and locks.
+`bim.edit_link` and the explicit save step are **removed**; cancel/restore semantics
+no longer exist (undo or move it back). The save math lives in
+`tool.Project.save_link_transformation`. Enable/disable take a `link_index`
+(default −1 = active link) so several links can be edited at once and script calls
+stay compatible.
+
+### Explore tool + append fixes for moved links
+
+- Highlight triangles come from `mesh.calc_loop_triangles()` filtered to the queried
+  element's polygon range (ngon-safe); edges keep `polygon.edge_keys` (no diagonals).
+- `get_selected_geometry` converts the ID-prop round trip to plain tuples (GPU
+  rejects `IDPropertyArray`); TRIS drawing gated on its own data.
+- `QueryLinkedElement` passes the ray-cast instance matrix through;
+  `find_obj_root` compares it against `empty @ obj_local` and falls back to the
+  collection's only instance when no matrix is available (select-by-GUID flow).
+- `bim.append_inspected_linked_element` pre-multiplies the imported object's matrix by
+  `calculate_link_delta_matrix(link)`, matching the link by the queried instance's
+  root empty first (filepath alone is ambiguous with several links per file). The
+  element's IFC placement syncs to the moved location on save — intended.
+
+### Drawings (`create_drawing`) — moved links and per-link queries
+
+- The linework serializer opened linked IFCs raw, so a moved link's elements were
+  drawn at their *original* coordinates (usually outside the drawing extents —
+  "linked objects disappear from prints after moving the link").
+- The stored link transformation is already the **model-space** delta (that is how
+  `save_link_transformation` derives it), which is exactly the space the serializer
+  works in — so it can be baked straight into the geometry iterator via the existing
+  `model-offset`/`model-rotation` settings. The mapping composes
+  `Trans(model-offset) @ Rot(model-rotation)` (see `mapping.cpp`), matching the
+  `Trans(t) @ Rot(R)` decomposition of the rigid link matrix; `model-rotation` is a
+  quaternion passed as `(x, y, z, w)`. The pre-existing 2mm plan-view Z-offset simply
+  adds onto the translation (translations commute).
+- The serialization loop previously collected files in a dict keyed by filepath, which
+  **collapsed same-file links into one pass** (one transform — the last link's — and
+  no query awareness): with two links of one file, only one showed in the drawing.
+  It now iterates one entry per link (`(path, file, transform, query)` tuples), and
+  intersects each link's drawing elements with
+  `ifcopenshell.util.selector.filter_elements(ifc, link.query)` so the drawing shows
+  what that link actually displays in the viewport.
+- `tool.Project.get_link_transformation_matrix(link)` is the shared accessor for the
+  stored 4×4 (None when identity/absent).
+- Verified headless with the window/door kit: moved window offset in the SVG by
+  exactly 5m × scale; unmoved door at its native position; both links present.
+
+### Drawings — `.cut` styling for linked models (BISECT cut mode)
+
+- The default **BISECT** cut mode deletes the OpenCASCADE serializer's cut linework
+  (`remove_cut_linework`) and regenerates cuts by bisecting **Blender mesh objects**
+  (`generate_bisect_linework` over `context.visible_objects`). Linked models are
+  instanced collections with no mesh objects, so their cuts were deleted and never
+  regenerated — linked elements only ever appeared as `projection`, and the `.cut`
+  CSS rule never applied to them. Long-standing gap, unrelated to moved links
+  (A/B-tested against pre-branch code: identical).
+- Fix: `remove_cut_linework` only removes cut groups whose guid resolves in the
+  **host** file — linked elements keep the serializer's cut geometry, which the
+  merge step then classes as `cut`.
+- **Cross-file STEP-id collision**: `tool.Ifc.get_object(linked_entity)` resolves the
+  entity's STEP id against the *host* session's id map and can return an arbitrary
+  host object (in the test project: the drawing camera, crashing
+  `generate_material_layers` with "expected 'Mesh' found 'Camera'"). Guarded via
+  `element.file is tool.Ifc.get()` in `generate_material_layers` and the merge step.
+- **Paint order**: the projection-under-cut convention was enforced only in
+  OPENCASCADE mode (`move_projection_to_bottom`); BISECT appends its own cut paths
+  last so it never needed it — but the retained serializer cuts of linked models are
+  emitted *before* the projections. BISECT now runs the same pass; `BringToFront`
+  (`move_elements_to_top`) still gets the final say.
+- Known limitation: linked cut paths are raw serializer output — they skip the
+  shapely path-closing/merging and the material-layer hatching pass (both need host
+  Blender objects). Stroke + fill from `.cut` CSS apply; layered hatching inside
+  linked cuts is a candidate follow-up.
+- 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).**
+  `get_linked_models_documents()` keyed documents by the *stored* `Location`, so
+  linking the same file first relative then absolute (or vice versa) created a second
+  `IfcDocumentInformation`. Both sides of the lookup now normalize through
+  `tool.Ifc.resolve_uri()` before matching.
+- **`Description` for the query — kept.** It is implementation metadata in an IFC
+  attribute, but consistent with the existing convention on these same references
+  (`Identification` stores the 4×4 transformation, a bigger stretch). References are
+  Bonsai-managed (`Scope="LINKED_MODEL"`), so user-description collisions are unlikely.
+  A cleaner consolidated convention (query + transform + options in one serialized
+  attribute) is a candidate follow-up, deliberately out of scope here.
+- **`md5(query)[:8]` — kept.** 32 bits ≈ birthday collision at ~65k distinct queries
+  *per file*; and a collision is not silent: the cache JSON stores the full query and
+  `should_clear_cache()` compares it, so a colliding cache is detected and rebuilt
+  (self-healing).
+- **Depsgraph autosave vs save-on-lock — autosave kept.** Save-on-lock alone loses the
+  "what you see is what's saved" guarantee (move + save project without locking =
+  silently dropped move) and loses undo tracking (undo fires a depsgraph update that
+  re-saves the reverted transform). The handler early-outs when no links exist and only
+  works on ticks containing an object-transform update while a link is unlocked.
+
+## Status — implemented (verified in Blender, incl. headless + GUI repro runs)
+
+Six commits on `Linked_File_Features`:
+
+- `0096c0f6a2` reload_link without a query preserves the stored one.
+- `40db55e52d` external styles + layerset slicing for linked models
+  (`project/operator.py`, `tool/loader.py`).
+- `d210d4c814` full Reload Link dialog + `bim.select_link_filepath`.
+- `3dc161f0f2` per-row lock toggle, auto-save handler, `edit_link` removed
+  (`project/operator.py`, `project/ui.py`, `project/__init__.py`, `tool/project.py`).
+- `0571d22855` Explore highlight (ngons, IDPropertyArray), moved-link highlight,
+  append placement (`tool/project.py`, `project/operator.py`, `project/decorator.py`).
+- `c14592ec0a` per-query caches, Description persistence, SKIP_SAVE.
+
+Plus:
+
+- `ee43ed5526` review-round path normalization in `get_linked_models_documents` /
+  `LinkIfc` (see Review round 1).
+- `1669cbcd43` drawing support for moved links and per-link queries in
+  `create_drawing` (`drawing/operator.py`, `tool/project.py`).
+- `.cut` styling for linked models in BISECT cut mode + STEP-id collision guards +
+  paint order (`drawing/operator.py`) — committed together with this note update.
+
+End-to-end verified with a two-links-one-file kit (window/door, distinct queries):
+correct visuals on load, after save → reopen → reload, in both headless and windowed
+Blender.
+
+## Things to test / verify
+
+- **IFC2X3 host**: `Description` doesn't exist — link queries silently not restored on
+  reopen (legacy fallback only for single-link files). Acceptable? Warn?
+- **Relative-path links** (`use_relative_path`) through the whole cycle: cache paths,
+  reference `Location`, reload path change, query restore. The duplicate-document case
+  (same file linked relative then absolute) is fixed — verify one document with two
+  references via `IfcDocumentInformation.HasDocumentReferences`.
+- Same file linked twice, **both moved differently**: Explore highlight and append
+  placement per instance (root-empty matching), per-link visibility toggles.
+- External styles with **image textures**: paths relative to the style's source
+  `.blend` may not resolve from the cache blend's location (shared limitation with the
+  normal import path).
+- Stale cache orphans: per-query filenames accumulate one blend+json pair per distinct
+  query next to the IFC; nothing auto-deletes them. Cleanup on unlink? Document?
+- Mid-drag auto-save writes the IFC reference outside Bonsai's transaction system —
+  confirm no undo-stack weirdness in longer editing sessions.
+- Layerset slicing on meshes shared by elements with *different* usages (offset/sense)
+  bakes the first element's slice — same as normal import, but worth a look with types.
+- `bim.select_link_filepath` round trip when the reload dialog was opened for a
+  non-active link, and dialog-state carry-over after editing the query *then* browsing.
+- **Drawing SVG guid cache vs moved links**: `create_drawing` skips elements whose
+  guids already exist in the drawing's SVG (`cached_linework`, invalidated only for
+  *edited host objects*). Moving a link does not invalidate its elements, so a
+  regenerated drawing keeps their old positions until the SVG is deleted. Candidate
+  fix: subtract a moved link's guids from `cached_linework` (compare stored transform
+  against the one recorded at last generation).
+- Same element appearing in two links of one file (overlapping queries) serializes
+  twice with different transforms; the SVG guid cache keeps whichever came first on
+  regeneration. Degenerate case — probably fine to ignore, but note it.

src/bonsai/bonsai/bim/module/drawing/operator.py

@@ -602,7 +602,7 @@ class CreateDrawing(bpy.types.Operator):
         context_type: Literal["body", "annotation"],
         drawing_elements: set[ifcopenshell.entity_instance],
         target_view: str,
-        link_matrix: Optional[Matrix] = None,
+        link_transform: Optional[np.ndarray] = None,
     ) -> None:
         drawing_elements = drawing_elements.copy()
         contexts_: list[list[int]] = getattr(contexts, context_type)
@@ -614,19 +614,22 @@ class CreateDrawing(bpy.types.Operator):
                 geom_settings.set("dimensionality", ifcopenshell.ifcopenshell_wrapper.CURVES_SURFACES_AND_SOLIDS)
                 geom_settings.set("iterator-output", ifcopenshell.ifcopenshell_wrapper.NATIVE)
 
-                is_plan = ifc.by_id(context[0]).ContextType == "Plan" and "PLAN_VIEW" in target_view
-                z_offset = (0.002 if target_view == "PLAN_VIEW" else -0.002) if is_plan else 0.0
-
-                if link_matrix is not None:
-                    unit_scale = ifcopenshell.util.unit.calculate_unit_scale(ifc)
-                    t = link_matrix.to_translation()
-                    offset = (t.x / unit_scale, t.y / unit_scale, t.z / unit_scale + z_offset)
-                    geom_settings.set("model-offset", offset)
-                    q = link_matrix.to_quaternion()
-                    geom_settings.set("model-rotation", (q.x, q.y, q.z, q.w))
-                elif z_offset:
+                offset = np.zeros(3)
+                if ifc.by_id(context[0]).ContextType == "Plan" and "PLAN_VIEW" in target_view:
                     # A 2mm Z offset to combat Z-fighting in plan or RCPs
-                    geom_settings.set("model-offset", (0.0, 0.0, z_offset))
+                    offset[2] = 0.002 if target_view == "PLAN_VIEW" else -0.002
+                if link_transform is not None:
+                    # Bake a moved link's transformation into the geometry. The
+                    # mapping composes Trans(model-offset) @ Rot(model-rotation),
+                    # matching the Trans(t) @ Rot(R) decomposition of the rigid
+                    # link matrix, so the Z offset above simply adds on.
+                    offset += link_transform[:3, 3]
+                    quaternion = Matrix(link_transform.tolist()).to_quaternion()
+                    geom_settings.set(
+                        "model-rotation", (quaternion.x, quaternion.y, quaternion.z, quaternion.w)
+                    )
+                if offset.any():
+                    geom_settings.set("model-offset", tuple(float(o) for o in offset))
 
                 geom_settings.set("context-ids", context)
                 it = ifcopenshell.geom.iterator(
@@ -679,6 +682,10 @@ class CreateDrawing(bpy.types.Operator):
             if "projection" in el.get("class", "").split():
                 continue
             element = self.get_element_by_guid(el.get("{http://www.ifcopenshell.org/ns}guid"))
+            if element is None or element.file is not tool.Ifc.get():
+                # Linked model element - no Blender object to bisect, and its
+                # STEP id must not be resolved against the host session.
+                continue
             if not (obj := tool.Ifc.get_object(element)):
                 continue
             if not (material := ifcopenshell.util.element.get_material(element)):
@@ -934,16 +941,25 @@ class CreateDrawing(bpy.types.Operator):
 
         bim_props = tool.Blender.get_bim_props()
         prefs = tool.Blender.get_addon_preferences()
-        # Map ifc_path → (ifc_file, link_matrix); main file has no link_matrix (None)
-        files: dict[str, tuple[ifcopenshell.file, Optional[Matrix]]] = {bim_props.ifc_file: (tool.Ifc.get(), None)}
 
         props = tool.Project.get_project_props()
+        # One entry per file *and* per link - the same file can be linked
+        # several times with different queries and transformations, so links
+        # cannot be collapsed into a dict keyed by filepath.
+        # Each entry is (path, file, link transformation or None, link query, link exclude).
+        file_entries: list[tuple[str, ifcopenshell.file, Optional[np.ndarray], str, str]] = [
+            (bim_props.ifc_file, tool.Ifc.get(), None, "", "")
+        ]
         for link in props.get_loaded_links_for_drawings():
-            try:
-                link_matrix = tool.Project.calculate_link_matrix(link)
-            except Exception:
-                link_matrix = None
-            files[link.filepath] = (self.get_linked_file(link), link_matrix)
+            file_entries.append(
+                (
+                    link.filepath,
+                    self.get_linked_file(link),
+                    tool.Project.get_link_transformation_matrix(link),
+                    link.query,
+                    link.exclude,
+                )
+            )
 
         target_view = ifcopenshell.util.element.get_psets(self.camera_element)["EPset_Drawing"]["TargetView"]
         self.setup_serialiser(target_view)
@@ -957,7 +973,7 @@ class CreateDrawing(bpy.types.Operator):
         raycast_objs = set()
         elements_with_faces = set()
 
-        for ifc_path, (ifc, link_matrix) in files.items():
+        for ifc_path, ifc, link_transform, link_query, link_exclude in file_entries:
             # Don't use draw.main() just whilst we're prototyping and experimenting
             # TODO: hash paths are never used
             ifc_hash = hashlib.md5(ifc_path.encode("utf-8")).hexdigest()
@@ -965,6 +981,11 @@ class CreateDrawing(bpy.types.Operator):
 
             self.serialiser.setFile(ifc)
             drawing_elements = tool.Drawing.get_drawing_elements(self.camera_element, ifc_file=ifc)
+            if link_query:
+                # Draw only what the link's selector filter loaded in the viewport.
+                drawing_elements &= ifcopenshell.util.selector.filter_elements(ifc, link_query)
+            if link_exclude:
+                drawing_elements -= ifcopenshell.util.selector.filter_elements(ifc, link_exclude)
 
             if self.cprops.fill_mode == "SHAPELY":
                 for element in drawing_elements.copy():
@@ -980,8 +1001,12 @@ class CreateDrawing(bpy.types.Operator):
             # A drawing prioritises a target view context first, followed by a model view context as a fallback.
             # Specifically for PLAN_VIEW and REFLECTED_PLAN_VIEW, any Plan context is also prioritised.
             contexts = self.get_linework_contexts(ifc, target_view)
-            self.serialize_contexts_elements(ifc, tree, contexts, "body", drawing_elements, target_view, link_matrix)
-            self.serialize_contexts_elements(ifc, tree, contexts, "annotation", drawing_elements, target_view, link_matrix)
+            self.serialize_contexts_elements(
+                ifc, tree, contexts, "body", drawing_elements, target_view, link_transform
+            )
+            self.serialize_contexts_elements(
+                ifc, tree, contexts, "annotation", drawing_elements, target_view, link_transform
+            )
 
             if tool.Ifc.get() == ifc and self.camera_element not in drawing_elements:
                 with profile("Camera element"):
@@ -1036,6 +1061,10 @@ class CreateDrawing(bpy.types.Operator):
             if self.cprops.generate_material_layers:
                 self.generate_material_layers(context, root)
             self.merge_linework_and_add_metadata(root)
+            # Bisect cut linework is appended after the projections, but the
+            # retained serializer cuts of linked models precede them - enforce
+            # the projection-under-cut convention like OPENCASCADE mode does.
+            self.move_projection_to_bottom(root)
             self.move_elements_to_top(root)
         elif self.cprops.cut_mode == "OPENCASCADE":
             self.move_projection_to_bottom(root)
@@ -1431,9 +1460,21 @@ class CreateDrawing(bpy.types.Operator):
                     continue
 
     def remove_cut_linework(self, root):
+        """Remove host elements' cut linework so bisecting can regenerate it.
+
+        Linked model elements keep the serializer's cut geometry - bisect
+        linework is generated from Blender mesh objects, and linked models
+        are instanced collections without any.
+        """
+        ifc_file = tool.Ifc.get()
         for el in root.findall(".//{http://www.w3.org/2000/svg}g[@{http://www.ifcopenshell.org/ns}guid]"):
-            if "projection" not in el.get("class", "").split():
-                el.getparent().remove(el)
+            if "projection" in el.get("class", "").split():
+                continue
+            try:
+                ifc_file.by_guid(el.get("{http://www.ifcopenshell.org/ns}guid"))
+            except RuntimeError:
+                continue  # Linked model element.
+            el.getparent().remove(el)
 
     def merge_linework_and_add_metadata(self, root):
         join_criteria = ifcopenshell.util.element.get_pset(self.camera_element, "EPset_Drawing", "JoinCriteria")
@@ -1468,7 +1509,9 @@ class CreateDrawing(bpy.types.Operator):
                 classes.append("cut")
                 el.set("class", " ".join(classes))
 
-            obj = tool.Ifc.get_object(element)
+            # Resolving a linked element's STEP id against the host session
+            # would return an arbitrary host object.
+            obj = tool.Ifc.get_object(element) if element is not None and element.file is tool.Ifc.get() else None
 
             if not obj:  # This is a linked model object. For now, do nothing.
                 continue

src/bonsai/bonsai/bim/module/project/__init__.py

@@ -45,7 +45,6 @@ classes = (
     operator.DisableEditingHeader,
     operator.DisableEditingLink,
     operator.EditHeader,
-    operator.EditLink,
     operator.EditProjectLibrary,
     operator.EnableCulling,
     operator.EnableEditingHeader,
@@ -67,6 +66,7 @@ classes = (
     operator.QueryLinkedElement,
     operator.RefreshClippingPlanes,
     operator.RefreshLibrary,
+    operator.ReloadAllLinks,
     operator.ReloadLink,
     operator.RemoveProjectLibrary,
     operator.RevertProject,
@@ -74,6 +74,7 @@ classes = (
     operator.SaveLibraryFile,
     operator.SelectLibraryFile,
     operator.SelectLinkedModelElement,
+    operator.SelectLinkFilepath,
     operator.SelectLinkHandle,
     operator.ToggleFilterCategories,
     operator.ToggleLinkSelectability,
@@ -109,12 +110,45 @@ classes = (
 addon_keymaps = []
 
 
+@bpy.app.handlers.persistent
+def _autosave_link_transforms(scene, depsgraph):
+    """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()
+    if not props.links:
+        return
+    handles = None
+    for update in depsgraph.updates:
+        if not update.is_updated_transform or not isinstance(update.id, bpy.types.Object):
+            continue
+        if handles is None:
+            # Built lazily so ticks without transform updates stay cheap.
+            handles = {}
+            for link in props.links:
+                if link.is_loaded and link.is_editing and (handle := tool.Project.get_link_empty_handle(link)):
+                    handles[handle] = link
+            if not handles:
+                return
+        if link := handles.get(update.id.original):
+            tool.Project.save_link_transformation(link)
+
+
 def register():
     if not bpy.app.background:
         bpy.utils.register_tool(workspace.ExploreTool, after={"builtin.transform"}, separator=True, group=False)
     bpy.types.Scene.BIMProjectProperties = bpy.props.PointerProperty(type=prop.BIMProjectProperties)
     bpy.types.Scene.MeasureToolSettings = bpy.props.PointerProperty(type=prop.MeasureToolSettings)
     bpy.app.handlers.load_post.append(decorator.toggle_decorations_on_load)
+    if _autosave_link_transforms not in bpy.app.handlers.depsgraph_update_post:
+        bpy.app.handlers.depsgraph_update_post.append(_autosave_link_transforms)
     bpy.types.TOPBAR_MT_file_import.append(ui.file_import_menu)
     bpy.types.TOPBAR_MT_file.prepend(ui.file_menu)
     bpy.types.TOPBAR_MT_file_context_menu.prepend(ui.file_menu)
@@ -139,6 +173,8 @@ def unregister():
     del bpy.types.Scene.BIMProjectProperties
     del bpy.types.Scene.MeasureToolSettings
     bpy.app.handlers.load_post.remove(decorator.toggle_decorations_on_load)
+    if _autosave_link_transforms in bpy.app.handlers.depsgraph_update_post:
+        bpy.app.handlers.depsgraph_update_post.remove(_autosave_link_transforms)
     bpy.types.TOPBAR_MT_file.remove(ui.file_menu)
     bpy.types.TOPBAR_MT_file_context_menu.remove(ui.file_menu)
 

src/bonsai/bonsai/bim/module/project/decorator.py

@@ -99,6 +99,7 @@ class ProjectDecorator:
 
         if geom.selected_edges:
             self.draw_batch("LINES", selected_vertices, selected_elements_color, geom.selected_edges)
+        if geom.selected_tris:
             self.draw_batch(
                 "TRIS", selected_vertices, tool.Blender.transparent_color(selected_elements_color), geom.selected_tris
             )

src/bonsai/bonsai/bim/module/project/operator.py

@@ -1360,10 +1360,18 @@ class LinkIfc(bpy.types.Operator, ImportHelper, tool.Ifc.Operator):
     )
     use_cache: bpy.props.BoolProperty(name="Use Cache", default=True)
     query: bpy.props.StringProperty(
-        name="Query",
+        name="Include",
         description=(
-            "Custom selector query to use to load element from a linked model. E.g. 'IfcElement'.\n\n"
-            "Default query - IfcElement, but excluding IfcProxy, IfcSpatialStructureElement, IfcSpatialElement, IfcFeatureElement."
+            "Selector query for the elements to load from the linked model. E.g. 'IfcElement'.\n\n"
+            "Default when empty - IfcElement, but excluding IfcProxy, IfcSpatialStructureElement, IfcSpatialElement, IfcFeatureElement."
+        ),
+    )
+    exclude: bpy.props.StringProperty(
+        name="Exclude",
+        description=(
+            "Selector query whose matches are excluded from the loaded elements.\n\n"
+            "Applied on top of the query (or the default set), providing the set "
+            "difference a single query cannot express. E.g. 'IfcSlab, parent=\"X\"'."
         ),
     )
 
@@ -1377,6 +1385,7 @@ class LinkIfc(bpy.types.Operator, ImportHelper, tool.Ifc.Operator):
         use_relative_path: bool
         use_cache: bool
         query: str
+        exclude: str
 
     def draw(self, context):
         assert self.layout
@@ -1395,6 +1404,7 @@ class LinkIfc(bpy.types.Operator, ImportHelper, tool.Ifc.Operator):
             row = self.layout.row()
             row.prop(pprops, "project_north")
         self.layout.prop(self, "query", placeholder="IfcElement")
+        self.layout.prop(self, "exclude", placeholder='IfcSlab, parent="..."')
 
     def _execute(self, context):
         start = time.time()
@@ -1417,18 +1427,26 @@ class LinkIfc(bpy.types.Operator, ImportHelper, tool.Ifc.Operator):
 
             new = props.links.add()
             if tool.Ifc.get():
-                if not (document := existing_links.get(filepath)):
+                # Look up by resolved absolute path so a file already linked
+                # with a relative Location (or vice versa) reuses its document.
+                resolved_filepath = Path(tool.Ifc.resolve_uri(filepath)).as_posix()
+                if not (document := existing_links.get(resolved_filepath)):
                     document = ifcopenshell.api.document.add_information(tool.Ifc.get())
                     document.Name = Path(filepath).name
                     document.Scope = "LINKED_MODEL"
                 reference = ifcopenshell.api.document.add_reference(tool.Ifc.get(), information=document)
                 reference[1] = ",".join([str(o) for o in np.eye(4).flatten().tolist()])
                 reference.Location = filepath.replace("\\", "/")
+                # Persist the filter per reference (Description is IFC4+ only).
+                description = tool.Project.encode_link_filter(self.query, self.exclude, loaded=True)
+                if description and hasattr(reference, "Description"):
+                    reference.Description = description
                 new.ifc_definition_id = reference.id()
             new.name = filepath
             new.filepath = filepath
             new.query = self.query
-            bpy.ops.bim.load_link(link_index=-1, use_cache=self.use_cache, query=self.query)
+            new.exclude = self.exclude
+            bpy.ops.bim.load_link(link_index=-1, use_cache=self.use_cache, query=self.query, exclude=self.exclude)
 
 
 class UnlinkIfc(bpy.types.Operator, tool.Ifc.Operator):
@@ -1487,21 +1505,28 @@ class LoadLink(bpy.types.Operator, tool.Ifc.Operator):
     bl_options = {"REGISTER", "UNDO"}
     bl_description = "Load the selected file"
 
+    # SKIP_SAVE: Blender reuses an operator's last-used property values on the
+    # next interactive invocation, which would leak one link's query/cache
+    # settings into another link's load.
     link_index: bpy.props.IntProperty(name="Link Index")
-    use_cache: bpy.props.BoolProperty(name="Use Cache", default=True)
-    query: bpy.props.StringProperty()
+    use_cache: bpy.props.BoolProperty(name="Use Cache", default=True, options={"SKIP_SAVE"})
+    query: bpy.props.StringProperty(options={"SKIP_SAVE"})
+    exclude: bpy.props.StringProperty(options={"SKIP_SAVE"})
 
     if TYPE_CHECKING:
         link_index: int
         use_cache: bool
         query: str
+        exclude: str
 
     def _execute(self, context):
         self.link = tool.Project.get_project_props().links[self.link_index]
-        # Fall back to the Link's stored query so callers that omit it
+        # Fall back to the Link's stored filter so callers that omit it
         # still replay the filter the link was created with.
         if not self.query and self.link.query:
             self.query = self.link.query
+        if not self.exclude and self.link.exclude:
+            self.exclude = self.link.exclude
         filepath = Path(tool.Ifc.resolve_uri(self.link.filepath))
         if not filepath.exists():
             self.report({"ERROR"}, f"File does not exist: '{filepath}'")
@@ -1538,22 +1563,21 @@ class LoadLink(bpy.types.Operator, tool.Ifc.Operator):
             self.link.is_loaded = False
 
     def link_ifc(self) -> Union[set[str], None]:
-        blend_filepath = self.filepath_.with_suffix(".ifc.cache.blend")
-        h5_filepath = self.filepath_.with_suffix(".ifc.cache.h5")
-        json_filepath = self.filepath_.with_suffix(".ifc.cache.json")
+        blend_filepath, json_filepath = tool.Project.get_link_cache_paths(self.filepath_, self.query, self.exclude)
 
         def should_clear_cache() -> bool:
             if not self.use_cache:
                 return True
             if not blend_filepath.exists():
                 return False
+            if not json_filepath.exists():
+                return True
             data = json.loads(json_filepath.read_text())
             # Empty 'query' - model loaded without custom query.
             # Missing 'query' - model was loaded before custom queries were introduced in Bonsai.
-            query = data.get("query", "")
-            return query != self.query
+            return data.get("query", "") != self.query or data.get("exclude", "") != self.exclude
 
-        if should_clear_cache():
+        if should_clear_cache() and blend_filepath.exists():
             os.remove(blend_filepath)
 
         if not blend_filepath.exists():
@@ -1581,7 +1605,7 @@ def run():
     pprops.project_north = "{pprops.project_north}"
     # Use absolute path to be safe from cwd changes.
     try:
-        bpy.ops.bim.load_linked_project(filepath=r"{str(self.filepath_)}", query={repr(self.query)})
+        bpy.ops.bim.load_linked_project(filepath=r"{str(self.filepath_)}", query={repr(self.query)}, exclude={repr(self.exclude)})
     except RuntimeError as e:
         # Operator failed (returned CANCELLED with error report)
         print(f"Failed to load linked project: {{e}}")
@@ -1630,7 +1654,7 @@ except Exception as e:
         if len(tool.Project.get_project_props().links) > 1:
             return  # Only the first link sets the origin
 
-        json_filepath = self.filepath_.with_suffix(".ifc.cache.json")
+        json_filepath = tool.Project.get_link_cache_paths(self.filepath_, self.query, self.exclude)[1]
         if not json_filepath.exists():
             return
 
@@ -1649,8 +1673,7 @@ except Exception as e:
         if not (crs_name := (ifcopenshell.util.geolocation.get_crs(tool.Ifc.get()) or {}).get("Name", "")):
             self.link.georeferenced = "NONE"
             return
-        reference = tool.Ifc.get().by_id(self.link.ifc_definition_id)
-        json_filepath = Path(reference.Location).with_suffix(".ifc.cache.json")
+        json_filepath = tool.Project.get_link_cache_paths(self.filepath_, self.query, self.exclude)[1]
         if not json_filepath.exists():
             self.link.georeferenced = "NONE"
             return
@@ -1662,43 +1685,211 @@ except Exception as e:
             self.link.georeferenced = "FULL_COMPATIBLE" if crs_name == data["model_crs"] else "NOT_COMPATIBLE"
 
 
-class ReloadLink(bpy.types.Operator):
+class ReloadLink(bpy.types.Operator, tool.Ifc.Operator):
     bl_idname = "bim.reload_link"
     bl_label = "Reload Link"
     bl_options = {"REGISTER", "UNDO"}
-    bl_description = "Reload the selected file"
+    bl_description = "Reload the selected file, optionally changing its file path and load options"
 
+    # SKIP_SAVE: this operator distinguishes "provided" from "unset" properties
+    # via is_property_set, so last-used property retention between interactive
+    # invocations would leak one link's settings into another's reload.
     link_index: bpy.props.IntProperty(name="Link Index")
+    filepath: bpy.props.StringProperty(
+        name="File Path",
+        description="Path to the linked IFC file",
+        options={"SKIP_SAVE"},
+    )
+    use_relative_path: bpy.props.BoolProperty(
+        name="Use Relative Path",
+        description="Whether to store linked model path relative to the currently opened IFC file.",
+        default=False,
+        options={"SKIP_SAVE"},
+    )
+    use_cache: bpy.props.BoolProperty(
+        name="Use Cache",
+        description="Reuse the cached geometry if it's still valid instead of reprocessing the IFC",
+        default=False,
+        options={"SKIP_SAVE"},
+    )
     query: bpy.props.StringProperty(
-        name="Query",
+        name="Include",
         description=(
-            "Custom selector query to use to load element from a linked model. E.g. 'IfcElement'.\n\n"
-            "Default query - IfcElement, but excluding IfcProxy, IfcSpatialStructureElement, IfcSpatialElement, IfcFeatureElement."
+            "Selector query for the elements to load from the linked model. E.g. 'IfcElement'.\n\n"
+            "Default when empty - IfcElement, but excluding IfcProxy, IfcSpatialStructureElement, IfcSpatialElement, IfcFeatureElement."
         ),
+        options={"SKIP_SAVE"},
+    )
+    exclude: bpy.props.StringProperty(
+        name="Exclude",
+        description=(
+            "Selector query whose matches are excluded from the loaded elements.\n\n"
+            "Applied on top of the query (or the default set), providing the set "
+            "difference a single query cannot express. E.g. 'IfcSlab, parent=\"X\"'."
+        ),
+        options={"SKIP_SAVE"},
     )
 
     if TYPE_CHECKING:
         link_index: int
+        filepath: str
+        use_relative_path: bool
+        use_cache: bool
         query: str
+        exclude: str
 
     def invoke(self, context, event):
         link = tool.Project.get_project_props().links[self.link_index]
-        self.query = link.query
+        # Properties may arrive pre-set when the dialog is reopened
+        # by bim.select_link_filepath - don't clobber them.
+        if not self.properties.is_property_set("filepath"):
+            self.filepath = link.filepath
+        if not self.properties.is_property_set("use_relative_path"):
+            self.use_relative_path = not Path(link.filepath).is_absolute()
+        if not self.properties.is_property_set("query"):
+            self.query = link.query
+        if not self.properties.is_property_set("exclude"):
+            self.exclude = link.exclude
         return context.window_manager.invoke_props_dialog(self)
 
     def draw(self, context):
         assert self.layout
+        pprops = tool.Project.get_project_props()
+        row = self.layout.row(align=True)
+        row.prop(self, "filepath")
+        op = row.operator("bim.select_link_filepath", text="", icon="FILEBROWSER")
+        op.link_index = self.link_index
+        # Carry the current dialog state through the file browser round-trip.
+        op.use_relative_path = self.use_relative_path
+        op.use_cache = self.use_cache
+        op.query = self.query
+        op.exclude = self.exclude
+        row = self.layout.row()
+        row.prop(self, "use_relative_path")
+        row = self.layout.row()
+        row.prop(self, "use_cache")
+        row = self.layout.row()
+        row.label(text="False Origin Mode:")
+        row = self.layout.row()
+        row.prop(pprops, "false_origin_mode", text="")
+        if pprops.false_origin_mode == "MANUAL":
+            row = self.layout.row()
+            row.prop(pprops, "false_origin")
+            row = self.layout.row()
+            row.prop(pprops, "project_north")
         self.layout.prop(self, "query", placeholder="IfcElement")
+        self.layout.prop(self, "exclude", placeholder='IfcSlab, parent="..."')
 
-    def execute(self, context):
+    def _execute(self, context):
         link = tool.Project.get_project_props().links[self.link_index]
-        # An unset query means the operator was called without the dialog
-        # (e.g. from a script) - preserve the link's stored query instead
-        # of overwriting it with the empty default.
+        # Unset properties mean the operator was called without the dialog
+        # (e.g. from a script) - preserve the link's stored values instead
+        # of overwriting them with the defaults.
         if self.properties.is_property_set("query"):
             link.query = self.query
+        if self.properties.is_property_set("exclude"):
+            link.exclude = self.exclude
+
+        filepath = self.filepath if self.properties.is_property_set("filepath") else link.filepath
+        if self.properties.is_property_set("use_relative_path"):
+            use_relative_path = self.use_relative_path
+        else:
+            use_relative_path = not Path(link.filepath).is_absolute()
+
+        abs_filepath = Path(tool.Ifc.resolve_uri(filepath))
+        if not abs_filepath.exists():
+            self.report({"ERROR"}, f"File does not exist: '{abs_filepath}'")
+            return {"CANCELLED"}
+        filepath = tool.Ifc.get_uri(abs_filepath, use_relative_path=use_relative_path)
+        if filepath != link.filepath:
+            link.name = filepath
+            link.filepath = filepath
+            if tool.Ifc.get() and link.ifc_definition_id:
+                reference = tool.Ifc.get().by_id(link.ifc_definition_id)
+                reference.Location = filepath.replace("\\", "/")
+                if document := tool.Document.get_reference_document(reference):
+                    document.Name = Path(filepath).name
+        if tool.Ifc.get() and link.ifc_definition_id:
+            reference = tool.Ifc.get().by_id(link.ifc_definition_id)
+            if hasattr(reference, "Description"):
+                reference.Description = tool.Project.encode_link_filter(
+                    link.query, link.exclude, loaded=True, display_name=link.display_name
+                )
+
         bpy.ops.bim.unload_link(link_index=self.link_index)
-        return bpy.ops.bim.load_link(link_index=self.link_index, use_cache=False, query=link.query) or {"FINISHED"}
+        return bpy.ops.bim.load_link(
+            link_index=self.link_index, use_cache=self.use_cache, query=link.query, exclude=link.exclude
+        ) or {"FINISHED"}
+
+
+class ReloadAllLinks(bpy.types.Operator):
+    bl_idname = "bim.reload_all_links"
+    bl_label = "Reload All Links"
+    bl_options = {"REGISTER", "UNDO"}
+    bl_description = "Reload all loaded linked models from disk, rebuilding their caches"
+
+    @classmethod
+    def poll(cls, context):
+        if not any(link.is_loaded for link in tool.Project.get_project_props().links):
+            cls.poll_message_set("No loaded links to reload.")
+            return False
+        return True
+
+    def execute(self, context):
+        props = tool.Project.get_project_props()
+        reloaded = 0
+        for i, link in enumerate(props.links):
+            if not link.is_loaded:
+                continue
+            # Called without filter properties, reload_link preserves each
+            # link's stored path, query and exclude.
+            bpy.ops.bim.reload_link(link_index=i)
+            reloaded += 1
+        self.report({"INFO"}, f"Reloaded {reloaded} linked model(s).")
+        return {"FINISHED"}
+
+
+class SelectLinkFilepath(bpy.types.Operator):
+    bl_idname = "bim.select_link_filepath"
+    bl_label = "Select Link File Path"
+    bl_options = {"REGISTER", "UNDO", "INTERNAL"}
+    bl_description = "Select a new file path for the linked model and return to the reload dialog"
+
+    link_index: bpy.props.IntProperty(name="Link Index")
+    filepath: bpy.props.StringProperty(subtype="FILE_PATH", options={"SKIP_SAVE", "HIDDEN"})
+    filter_glob: bpy.props.StringProperty(default="*.ifc", options={"HIDDEN"})
+    # Reload dialog state carried through the file browser round-trip.
+    use_relative_path: bpy.props.BoolProperty(options={"HIDDEN"})
+    use_cache: bpy.props.BoolProperty(options={"HIDDEN"})
+    query: bpy.props.StringProperty(options={"HIDDEN"})
+    exclude: bpy.props.StringProperty(options={"HIDDEN"})
+
+    if TYPE_CHECKING:
+        link_index: int
+        filepath: str
+        filter_glob: str
+        use_relative_path: bool
+        use_cache: bool
+        query: str
+        exclude: str
+
+    def invoke(self, context, event):
+        link = tool.Project.get_project_props().links[self.link_index]
+        self.filepath = tool.Ifc.resolve_uri(link.filepath)
+        context.window_manager.fileselect_add(self)
+        return {"RUNNING_MODAL"}
+
+    def execute(self, context):
+        bpy.ops.bim.reload_link(
+            "INVOKE_DEFAULT",
+            link_index=self.link_index,
+            filepath=self.filepath,
+            use_relative_path=self.use_relative_path,
+            use_cache=self.use_cache,
+            query=self.query,
+            exclude=self.exclude,
+        )
+        return {"FINISHED"}
 
 
 class ToggleLinkSelectability(bpy.types.Operator):
@@ -1716,7 +1907,7 @@ class ToggleLinkSelectability(bpy.types.Operator):
         props = tool.Project.get_project_props()
         link = props.links[self.link_index]
         self.library_filepath = tool.Blender.ensure_blender_path_is_abs(
-            Path(link.filepath).with_suffix(".ifc.cache.blend")
+            tool.Project.get_link_cache_paths(link.filepath, link.query, link.exclude)[0]
         )
         link.is_selectable = (is_selectable := not link.is_selectable)
         for collection in self.get_linked_collections():
@@ -1753,7 +1944,7 @@ class ToggleLinkVisibility(bpy.types.Operator):
         props = tool.Project.get_project_props()
         link = props.links[self.link_index]
         self.library_filepath = tool.Blender.ensure_blender_path_is_abs(
-            Path(link.filepath).with_suffix(".ifc.cache.blend")
+            tool.Project.get_link_cache_paths(link.filepath, link.query, link.exclude)[0]
         )
         if self.mode == "WIREFRAME":
             self.toggle_wireframe(link)
@@ -1795,10 +1986,16 @@ class EnableEditingLink(bpy.types.Operator):
     bl_idname = "bim.enable_editing_link"
     bl_label = "Enable Editing Link"
     bl_options = {"REGISTER", "UNDO"}
-    bl_description = "Enable editing link location"
+    bl_description = "Unlock the link's position for editing. Any movement is saved automatically"
+
+    link_index: bpy.props.IntProperty(name="Link Index", default=-1)
+
+    if TYPE_CHECKING:
+        link_index: int
 
     def execute(self, context):
-        link = tool.Project.get_project_props().active_link
+        props = tool.Project.get_project_props()
+        link = props.active_link if self.link_index == -1 else props.links[self.link_index]
         assert link
         link.is_editing = True
         obj = tool.Project.get_link_empty_handle(link)
@@ -1807,70 +2004,25 @@ class EnableEditingLink(bpy.types.Operator):
         return {"FINISHED"}
 
 
-class DisableEditingLink(bpy.types.Operator):
+class DisableEditingLink(bpy.types.Operator, tool.Ifc.Operator):
     bl_idname = "bim.disable_editing_link"
     bl_label = "Disable Editing Link"
     bl_options = {"REGISTER", "UNDO"}
-    bl_description = "Disable editing link and restore to previously saved location"
+    bl_description = "Lock the link at its current location"
 
-    def execute(self, context):
-        link = tool.Project.get_project_props().active_link
-        assert link
-        link.is_editing = False
-        obj = tool.Project.get_link_empty_handle(link)
-        assert obj
-        obj.matrix_world = tool.Project.calculate_link_matrix(link)
-        tool.Geometry.lock_object(obj)
-        return {"FINISHED"}
+    link_index: bpy.props.IntProperty(name="Link Index", default=-1)
 
-
-class EditLink(bpy.types.Operator, tool.Ifc.Operator):
-    bl_idname = "bim.edit_link"
-    bl_label = "Edit Link"
-    bl_options = {"REGISTER", "UNDO"}
-    bl_description = "Disable editing link and restore to previously saved location"
+    if TYPE_CHECKING:
+        link_index: int
 
     def _execute(self, context):
-        link = tool.Project.get_project_props().active_link
+        props = tool.Project.get_project_props()
+        link = props.active_link if self.link_index == -1 else props.links[self.link_index]
         assert link
         link.is_editing = False
         obj = tool.Project.get_link_empty_handle(link)
         assert obj
-        new_obj_matrix = obj.matrix_world
-
-        filepath = Path(tool.Ifc.resolve_uri(link.filepath))
-        with open(filepath.with_suffix(".ifc.cache.json"), "r") as f:
-            metadata = json.load(f)
-
-        rot = ifcopenshell.util.shape_builder.np_rotation_matrix(
-            radians(-float(metadata["model_project_north"])), 4, "Z"
-        )
-        global_matrix = rot @ np.eye(4)
-        global_matrix[:, 3][:3] = [float(o) for o in metadata["model_origin_si"].split(",")]
-
-        gprops = tool.Georeference.get_georeference_props()
-        rot = ifcopenshell.util.shape_builder.np_rotation_matrix(radians(-float(gprops.model_project_north)), 4, "Z")
-        local_matrix = rot @ np.eye(4)
-        local_matrix[:, 3][:3] = [float(o) for o in gprops.model_origin_si.split(",")]
-
-        # obj_matrix is typically calculated as:
-        # obj_matrix = np.linalg.inv(local_matrix) @ transformation @ global_matrix
-        identity_blender_matrix = np.linalg.inv(local_matrix) @ global_matrix
-        if np.allclose(np.array(new_obj_matrix), identity_blender_matrix, atol=1e-5):
-            link.has_transformation = False
-            transformation = ",".join(map(str, np.eye(4).reshape(-1)))
-        else:
-            transformed_global_matrix = local_matrix @ np.array(new_obj_matrix)
-            transformation = transformed_global_matrix @ np.linalg.inv(global_matrix)
-            link.has_transformation = True
-            transformation = ",".join(map(str, transformation.reshape(-1)))
-
-        if tool.Ifc.get():
-            reference = tool.Ifc.get().by_id(link.ifc_definition_id)
-            reference[1] = transformation
-        else:
-            link.transformation = transformation
-
+        tool.Project.save_link_transformation(link)
         obj.matrix_world = tool.Project.calculate_link_matrix(link)
         tool.Geometry.lock_object(obj)
 
@@ -2012,6 +2164,8 @@ class ExportIFC(bpy.types.Operator, ExportHelper):
         # gizmo polls gate on each preview's is_active flag, and a stuck flag
         # persisted through the save would silently hide them on reload.
         preview_base.discard_pending_previews(context.scene)
+        # Links loaded and visible right now auto-load on the next open.
+        tool.Project.update_linked_models_state()
         # Suffix is appended to the IFC save-success report below so the auto-commit
         # info isn't immediately overwritten by the success message in Blender's
         # status bar (only the latest self.report({"INFO"}, ...) sticks).
@@ -2119,14 +2273,23 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
 
     query: bpy.props.StringProperty()
     """See ``bim.link_ifc``."""
+    exclude: bpy.props.StringProperty()
+    """See ``bim.link_ifc``."""
 
     if TYPE_CHECKING:
         query: str
+        exclude: str
 
     file: ifcopenshell.file
     meshes: dict[str, bpy.types.Mesh]
     # Material names is derived from diffuse as in 'r-g-b-a'.
     blender_mats: dict[str, bpy.types.Material]
+    # Materials appended from external .blend styles, keyed by style id.
+    # None means the style has no loadable external .blend style.
+    external_style_mats: dict[int, Union[bpy.types.Material, None]]
+    # Appended data-blocks keyed by (filepath, data_block_type, name)
+    # so styles sharing the same external material don't append duplicates.
+    appended_external_blocks: dict[tuple[str, str, str], Union[bpy.types.Material, None]]
 
     def invoke(self, context, event):
         # Invoke is for debugging purposes, users are not intended to use this method really.
@@ -2183,6 +2346,9 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
             else:
                 self.elements |= set(self.file.by_type("IfcSpatialElement"))
             self.elements -= set(self.file.by_type("IfcFeatureElement"))
+        if self.exclude:
+            # The set difference a single selector query cannot express.
+            self.elements -= ifcopenshell.util.selector.filter_elements(self.file, self.exclude)
 
         if tool.Loader.settings.false_origin_mode == "MANUAL" and tool.Loader.settings.false_origin:
             tool.Loader.set_manual_blender_offset(self.file)
@@ -2190,7 +2356,7 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
             tool.Loader.guess_false_origin(self.file)
 
         tool.Georeference.set_model_origin()
-        self.json_filepath = self.filepath + ".cache.json"
+        self.json_filepath = str(tool.Project.get_link_cache_paths(self.filepath, self.query, self.exclude)[1])
         data = {
             "model_is_georeferenced": gprops.model_is_georeferenced,
             "model_crs": gprops.model_crs,
@@ -2208,10 +2374,14 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
             "false_origin": pprops.false_origin,
             "project_north": pprops.project_north,
             "query": self.query,
+            "exclude": self.exclude,
         }
         with open(self.json_filepath, "w") as f:
             json.dump(data, f)
 
+        self.external_style_mats = {}
+        self.appended_external_blocks = {}
+
         for settings in tool.Loader.settings.context_settings:
             if not self.elements:
                 break
@@ -2251,8 +2421,10 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
                     mat = tuple(mat)
                     blender_mat = blender_mats.get(mat, None)
                     if not blender_mat:
-                        blender_mat = bpy.data.materials.new("Chunk")
-                        blender_mat.diffuse_color = mat
+                        blender_mat = self.get_external_material(int(mat[4]))
+                        if not blender_mat:
+                            blender_mat = bpy.data.materials.new("Chunk")
+                            blender_mat.diffuse_color = mat[:4]
                         blender_mats[mat] = blender_mat
                     mat_results.append(blender_mat)
 
@@ -2270,11 +2442,16 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
                 while True:  # Main loop.
                     shape = iterator.get()
                     assert isinstance(shape, W.TriangulationElement)
-                    results.add(self.file.by_id(shape.id))
+                    element = self.file.by_id(shape.id)
+                    results.add(element)
                     geometry = shape.geometry
 
-                    # Elements with a lot of geometry benefit from instancing to save memory
-                    if ifcopenshell.util.shape.get_faces(geometry).shape[0] > 333:  # 333 tris
+                    # Elements with a lot of geometry benefit from instancing to save memory.
+                    # Multi-layer elements also take this path as they need their own
+                    # local-space mesh to be sliced into per-layer materials.
+                    if ifcopenshell.util.shape.get_faces(geometry).shape[0] > 333 or self.is_multilayer_element(
+                        element
+                    ):  # 333 tris
                         self.process_occurrence(shape)
                         if not iterator.next():
                             if not chunked_verts:
@@ -2291,9 +2468,15 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
 
                     ms = np.vstack([default_mat, ifcopenshell.util.shape.get_material_colors(shape.geometry)])
                     mi = ifcopenshell.util.shape.get_faces_material_style_ids(shape.geometry)
+                    # Style ids ride along as a 5th column so styles with
+                    # external .blend materials survive the per-color dedup.
+                    style_ids = np.zeros((len(ms), 1))
                     for geom_material_idx, geom_material in enumerate(shape.geometry.materials):
                         if not geom_material.instance_id():
                             ms[geom_material_idx + 1] = (0.8, 0.8, 0.8, 1)
+                        elif self.get_external_material(geom_material.instance_id()):
+                            style_ids[geom_material_idx + 1] = geom_material.instance_id()
+                    ms = np.hstack((ms, style_ids))
                     chunked_materials.append(ms)
                     chunked_material_ids.append(mi + material_offset + 1)
                     material_offset += len(ms)
@@ -2380,12 +2563,14 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
                     diffuse = (material.diffuse.r(), material.diffuse.g(), material.diffuse.b(), alpha)
                 else:
                     diffuse = (0.8, 0.8, 0.8, 1)  # Blender's default material
-                material_name = f"{diffuse[0]}-{diffuse[1]}-{diffuse[2]}-{diffuse[3]}"
-                blender_mat = self.blender_mats.get(material_name, None)
+                blender_mat = self.get_external_material(material.instance_id())
                 if not blender_mat:
-                    blender_mat = bpy.data.materials.new(material_name)
-                    blender_mat.diffuse_color = diffuse
-                    self.blender_mats[material_name] = blender_mat
+                    material_name = f"{diffuse[0]}-{diffuse[1]}-{diffuse[2]}-{diffuse[3]}"
+                    blender_mat = self.blender_mats.get(material_name, None)
+                    if not blender_mat:
+                        blender_mat = bpy.data.materials.new(material_name)
+                        blender_mat.diffuse_color = diffuse
+                        self.blender_mats[material_name] = blender_mat
                 slot_index = mesh.materials.find(material.name)
                 if slot_index == -1:
                     mesh.materials.append(blender_mat)
@@ -2398,6 +2583,8 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
             mesh.polygons.foreach_set("material_index", material_index)
             mesh.update()
 
+            mesh = tool.Loader.slice_layerset_mesh(element, mesh, style_to_material=self.get_style_material)
+
             self.meshes[geometry.id] = mesh
 
         obj = bpy.data.objects.new(tool.Loader.get_name(element), mesh)
@@ -2410,6 +2597,88 @@ class LoadLinkedProject(bpy.types.Operator, ImportHelper):
 
         self.collection.objects.link(obj)
 
+    def get_external_material(self, style_id: int) -> Union[bpy.types.Material, None]:
+        """Get the Blender material referenced by a style's external .blend style, if it has one.
+
+        The material is appended from the external .blend file on first use and
+        cached, so it ends up saved inside the link's .cache.blend.
+        """
+        if not style_id:
+            return None
+        if style_id in self.external_style_mats:
+            return self.external_style_mats[style_id]
+
+        material = None
+        # instance_id may also refer to an IfcMaterial when the item has
+        # a material but no style, hence the class check.
+        style = self.file.by_id(style_id)
+        external = None
+        if style.is_a("IfcSurfaceStyle"):
+            external = next((s for s in style.Styles if s.is_a("IfcExternallyDefinedSurfaceStyle")), None)
+
+        if (
+            external
+            and external.Location
+            and external.Location.endswith(".blend")
+            and external.Identification
+            and "/" in external.Identification
+        ):
+            location = Path(external.Location)
+            if not location.is_absolute():
+                # Relative locations are relative to the linked IFC, not the host.
+                location = Path(self.filepath).parent / location
+            data_block_type, data_block = external.Identification.split("/", 1)
+            key = (str(location), data_block_type, data_block)
+            if key in self.appended_external_blocks:
+                material = self.appended_external_blocks[key]
+            elif not location.exists():
+                print(f"WARNING. External style file not found for {style}: '{location}'")
+                self.appended_external_blocks[key] = None
+            else:
+                db = tool.Blender.append_data_block(str(location), data_block_type, data_block)
+                material = db["data_block"]
+                if not isinstance(material, bpy.types.Material):
+                    print(f"WARNING. Failed to load external style for {style}: {db['msg'] or 'not a material'}")
+                    material = None
+                else:
+                    # The source .blend may have been authored in a Bonsai session -
+                    # unlink any stale IFC id so it's not misinterpreted here or in the host.
+                    tool.Style.get_material_style_props(material).ifc_definition_id = 0
+                self.appended_external_blocks[key] = material
+
+        self.external_style_mats[style_id] = material
+        return material
+
+    def is_multilayer_element(self, element: ifcopenshell.entity_instance) -> bool:
+        material = ifcopenshell.util.element.get_material(element)
+        return bool(
+            material and material.is_a("IfcMaterialLayerSetUsage") and len(material.ForLayerSet.MaterialLayers) > 1
+        )
+
+    def get_style_material(self, style: ifcopenshell.entity_instance) -> Union[bpy.types.Material, None]:
+        """Resolve a style to a Blender material for slice_layerset_mesh.
+
+        Prefers the style's external .blend material, falling back to a flat
+        diffuse material as used for the rest of the linked geometry.
+        """
+        if material := self.get_external_material(style.id()):
+            return material
+        # IfcSurfaceStyleRendering is a subclass of IfcSurfaceStyleShading.
+        shading = next((s for s in style.Styles if s.is_a("IfcSurfaceStyleShading")), None)
+        if shading:
+            colour = shading.SurfaceColour
+            alpha = 1.0 - (getattr(shading, "Transparency", None) or 0.0)
+            diffuse = (colour.Red, colour.Green, colour.Blue, alpha)
+        else:
+            diffuse = (0.8, 0.8, 0.8, 1.0)
+        material_name = f"{diffuse[0]}-{diffuse[1]}-{diffuse[2]}-{diffuse[3]}"
+        material = self.blender_mats.get(material_name, None)
+        if not material:
+            material = bpy.data.materials.new(material_name)
+            material.diffuse_color = diffuse
+            self.blender_mats[material_name] = material
+        return material
+
     def create_object(
         self,
         verts: np.ndarray,
@@ -2483,7 +2752,7 @@ class QueryLinkedElement(bpy.types.Operator):
 
         guid = tool.Project.Link.get_guid_by_face_index(obj, face_index)
         assert guid is not None
-        tool.Project.Link.select_linked_element(context, obj, guid)
+        tool.Project.Link.select_linked_element(context, obj, guid, instance_matrix)
 
         self.report({"INFO"}, f"Loaded data for {guid}")
         ProjectDecorator.install(bpy.context)
@@ -2608,6 +2877,27 @@ class AppendInspectedLinkedElement(AppendLibraryElement):
         if element_type and tool.Ifc.get_object(element_type) is None:
             self.import_type_from_ifc(element_type, context)
 
+        # If the link was moved, place the appended element where the link
+        # is displayed rather than at its original coordinates.
+        obj = tool.Ifc.get_object(element)
+        if isinstance(obj, bpy.types.Object):
+            # Prefer matching the link by the queried instance's root empty -
+            # the same file may be linked several times (different queries)
+            # and moved to different locations.
+            root = props.queried_obj_root
+            linked_filepath = Path(queried_obj["ifc_filepath"])
+            link_match = None
+            for link in props.links:
+                if root is not None and tool.Project.get_link_empty_handle(link) == root:
+                    link_match = link
+                    break
+                if link_match is None and Path(tool.Ifc.resolve_uri(link.filepath)) == linked_filepath:
+                    link_match = link
+            if link_match:
+                delta = tool.Project.calculate_link_delta_matrix(link_match)
+                if not delta.is_identity:
+                    obj.matrix_world = delta @ obj.matrix_world
+
         return {"FINISHED"}
 
 

src/bonsai/bonsai/bim/module/project/prop.py

@@ -261,8 +261,21 @@ class Link(PropertyGroup):
         default=0,
     )
     query: StringProperty(
-        name="Query",
-        description="Selector query used to filter elements when loading the linked model",
+        name="Include",
+        description="Selector query for the elements to load from the linked model",
+        default="",
+    )
+    exclude: StringProperty(
+        name="Exclude",
+        description="Selector query whose matches are excluded when loading the linked model",
+        default="",
+    )
+    display_name: StringProperty(
+        name="Name",
+        description=(
+            "Optional display name to tell links apart (e.g. when the same file "
+            "is linked several times). Shows the file path when empty"
+        ),
         default="",
     )
 
@@ -281,6 +294,8 @@ class Link(PropertyGroup):
         empty_handle: Union[bpy.types.Object, None]
         ifc_definition_id: int
         query: str
+        exclude: str
+        display_name: str
 
 
 class EditedObj(PropertyGroup):

src/bonsai/bonsai/bim/module/project/ui.py

@@ -492,17 +492,13 @@ class BIM_PT_links(Panel):
 
         row = self.layout.row(align=True)
         row.operator("bim.link_ifc")
+        row.operator("bim.reload_all_links", text="", icon="FILE_REFRESH")
         if self.props.links:
             if self.props.active_link:
                 row = self.layout.row(align=True)
                 row.alignment = "RIGHT"
                 index = self.props.active_link_index
                 if self.props.active_link.is_loaded:
-                    if self.props.active_link.is_editing:
-                        row.operator("bim.edit_link", text="", icon="CHECKMARK")
-                        row.operator("bim.disable_editing_link", text="", icon="CANCEL")
-                    else:
-                        row.operator("bim.enable_editing_link", text="", icon="GREASEPENCIL")
                     row.operator("bim.select_linked_model_element", icon="VIEWZOOM", text="")
                     row.operator("bim.select_link_handle", text="", icon="OBJECT_DATA").link_index = index
                     row.operator("bim.unload_link", text="", icon="UNLINKED").link_index = index
@@ -643,7 +639,12 @@ class BIM_UL_links(UIList):
             if item.has_transformation:
                 row.label(text="", icon="OBJECT_ORIGIN")
 
-            row.label(text=item.filepath)
+            # Double-click to rename; shows the file path while unset.
+            row.prop(item, "display_name", text="", emboss=False, placeholder=item.filepath)
+            if item.is_editing:
+                row.operator("bim.disable_editing_link", text="", icon="UNLOCKED", emboss=False).link_index = index
+            else:
+                row.operator("bim.enable_editing_link", text="", icon="LOCKED", emboss=False).link_index = index
             icon = "RESTRICT_SELECT_OFF" if item.is_selectable else "RESTRICT_SELECT_ON"
             row.operator("bim.toggle_link_selectability", text="", icon=icon, emboss=False).link_index = index
             icon = "CUBE" if item.is_wireframe else "MESH_CUBE"
@@ -655,7 +656,7 @@ class BIM_UL_links(UIList):
             op.link_index = index
             op.mode = "VISIBLE"
         else:
-            row.label(text=item.filepath)
+            row.prop(item, "display_name", text="", emboss=False, placeholder=item.filepath)
 
 
 class BIM_PT_purge(Panel):

src/bonsai/bonsai/tool/loader.py

@@ -23,7 +23,7 @@ import os
 import re
 from math import atan, radians
 from pathlib import Path
-from typing import Any, Optional, Union, cast
+from typing import Any, Callable, Optional, Union, cast
 
 import bmesh
 import bpy
@@ -1073,7 +1073,19 @@ class Loader(bonsai.core.tool.Loader):
         return mesh
 
     @classmethod
-    def slice_layerset_mesh(cls, element: ifcopenshell.entity_instance, mesh: bpy.types.Mesh) -> bpy.types.Mesh:
+    def slice_layerset_mesh(
+        cls,
+        element: ifcopenshell.entity_instance,
+        mesh: bpy.types.Mesh,
+        style_to_material: Optional[Callable[[ifcopenshell.entity_instance], Union[bpy.types.Material, None]]] = None,
+    ) -> bpy.types.Mesh:
+        """Bisect a layerset element's mesh at layer boundaries and assign each layer its material style.
+
+        :param style_to_material: Callback resolving an IfcSurfaceStyle to a Blender material.
+            Defaults to the IFC-linked material, which only works for the actively edited project.
+        """
+        if style_to_material is None:
+            style_to_material = tool.Ifc.get_object
         if not (material := ifcopenshell.util.element.get_material(element)):
             return mesh
         elif material.is_a("IfcMaterialLayerSetUsage"):
@@ -1121,7 +1133,8 @@ class Loader(bonsai.core.tool.Loader):
                 continue
             if (material_index := styles.get(style, None)) is None:
                 material_index = len(mesh.materials)
-                mesh.materials.append(tool.Ifc.get_object(style))
+                mesh.materials.append(style_to_material(style))
+                styles[style] = material_index
             if i == last_i:
                 for face in bisect_geom["geom"]:
                     if isinstance(face, bmesh.types.BMFace):

src/bonsai/bonsai/tool/project.py

@@ -18,6 +18,7 @@
 
 from __future__ import annotations
 
+import hashlib
 import json
 import os
 import shutil
@@ -89,10 +90,90 @@ class Project(bonsai.core.tool.Project):
         else:
             link.empty_handle = empty
 
+    @classmethod
+    def get_link_cache_paths(cls, filepath: Union[Path, str], query: str, exclude: str = "") -> tuple[Path, Path]:
+        """Get the (blend, json) cache paths for a linked model's filter.
+
+        Cache files are per-filter so the same IFC file can be linked several
+        times with different include/exclude queries without the caches
+        overwriting each other. An empty filter keeps the legacy un-suffixed
+        names, and an include-only filter keeps the pre-exclude hash so
+        existing caches stay valid.
+        """
+        filepath = Path(filepath)
+        if not query and not exclude:
+            suffix = ""
+        elif not exclude:
+            suffix = "." + hashlib.md5(query.encode("utf-8")).hexdigest()[:8]
+        else:
+            suffix = "." + hashlib.md5(f"{query}\0{exclude}".encode("utf-8")).hexdigest()[:8]
+        return (
+            filepath.with_suffix(f".ifc.cache{suffix}.blend"),
+            filepath.with_suffix(f".ifc.cache{suffix}.json"),
+        )
+
+    @classmethod
+    def encode_link_filter(
+        cls, query: str, exclude: str, loaded: bool = False, display_name: str = ""
+    ) -> Union[str, None]:
+        """Serialize a link's filter and state for IfcDocumentReference.Description.
+
+        A plain include query is stored as-is (backwards compatible); an
+        exclude, a loaded state or a display name promotes the value to a
+        small JSON blob. The loaded flag makes the link auto-load on the
+        next project open.
+        """
+        if exclude or loaded or display_name:
+            return json.dumps({"include": query, "exclude": exclude, "loaded": loaded, "name": display_name})
+        return query or None
+
+    @classmethod
+    def decode_link_filter(cls, description: Union[str, None]) -> tuple[str, str, bool, str]:
+        """Get (query, exclude, loaded, display_name) from a Description written by encode_link_filter."""
+        if not description:
+            return "", "", False, ""
+        if description.startswith("{"):
+            try:
+                data = json.loads(description)
+                if isinstance(data, dict):
+                    return (
+                        data.get("include", "") or "",
+                        data.get("exclude", "") or "",
+                        bool(data.get("loaded", False)),
+                        data.get("name", "") or "",
+                    )
+            except json.JSONDecodeError:
+                pass
+        return description, "", False, ""
+
+    @classmethod
+    def update_linked_models_state(cls) -> None:
+        """Persist each link's loaded/visible state onto its document reference.
+
+        Called at IFC save time so links that were loaded and visible
+        auto-load the next time the project is opened.
+        """
+        if not tool.Ifc.get():
+            return
+        for link in cls.get_project_props().links:
+            if not link.ifc_definition_id:
+                continue
+            try:
+                reference = tool.Ifc.get().by_id(link.ifc_definition_id)
+            except RuntimeError:
+                continue
+            if hasattr(reference, "Description"):
+                reference.Description = cls.encode_link_filter(
+                    link.query,
+                    link.exclude,
+                    loaded=link.is_loaded and not link.is_hidden,
+                    display_name=link.display_name,
+                )
+
     @classmethod
     def calculate_link_matrix(cls, link: Link) -> Matrix:
         filepath = Path(tool.Ifc.resolve_uri(link.filepath))
-        with open(filepath.with_suffix(".ifc.cache.json"), "r") as f:
+        with open(cls.get_link_cache_paths(filepath, link.query, link.exclude)[1], "r") as f:
             metadata = json.load(f)
 
         rot = ifcopenshell.util.shape_builder.np_rotation_matrix(
@@ -117,6 +198,86 @@ class Project(bonsai.core.tool.Project):
         local_matrix[:, 3][:3] = [float(o) for o in gprops.model_origin_si.split(",")]
         return Matrix(np.linalg.inv(local_matrix) @ global_matrix)
 
+    @classmethod
+    def get_link_transformation_matrix(cls, link: Link) -> Union[npt.NDArray[np.float64], None]:
+        """Get the link's saved 4x4 transformation in model coordinates, or None when identity."""
+        if tool.Ifc.get():
+            transformation = tool.Ifc.get().by_id(link.ifc_definition_id)[1]  # Identification
+        else:
+            transformation = link.transformation
+        if not transformation:
+            return None
+        matrix = np.fromstring(transformation, sep=",", dtype=np.float64).reshape(4, 4)
+        if np.allclose(matrix, np.eye(4)):
+            return None
+        return matrix
+
+    @classmethod
+    def calculate_link_delta_matrix(cls, link: Link) -> Matrix:
+        """Get the matrix mapping the link's unmoved world positions to its moved ones.
+
+        Returns identity when the link has no saved transformation.
+        """
+        if tool.Ifc.get():
+            transformation = tool.Ifc.get().by_id(link.ifc_definition_id)[1]  # Identification
+        else:
+            transformation = link.transformation
+
+        if not transformation:
+            return Matrix.Identity(4)
+        transformation = np.fromstring(transformation, sep=",", dtype=np.float64).reshape(4, 4)
+        if np.allclose(transformation, np.eye(4)):
+            return Matrix.Identity(4)
+
+        gprops = tool.Georeference.get_georeference_props()
+        rot = ifcopenshell.util.shape_builder.np_rotation_matrix(radians(-float(gprops.model_project_north)), 4, "Z")
+        local_matrix = rot @ np.eye(4)
+        local_matrix[:, 3][:3] = [float(o) for o in gprops.model_origin_si.split(",")]
+
+        # Link empty matrix is inv(local) @ transformation @ global (see
+        # calculate_link_matrix), so moved = inv(local) @ T @ local @ unmoved.
+        return Matrix(np.linalg.inv(local_matrix) @ transformation @ local_matrix)
+
+    @classmethod
+    def save_link_transformation(cls, link: Link) -> None:
+        """Persist the link handle's current world matrix as the link's saved transformation."""
+        obj = cls.get_link_empty_handle(link)
+        assert obj
+        new_obj_matrix = np.array(obj.matrix_world)
+
+        filepath = Path(tool.Ifc.resolve_uri(link.filepath))
+        with open(cls.get_link_cache_paths(filepath, link.query, link.exclude)[1], "r") as f:
+            metadata = json.load(f)
+
+        rot = ifcopenshell.util.shape_builder.np_rotation_matrix(
+            radians(-float(metadata["model_project_north"])), 4, "Z"
+        )
+        global_matrix = rot @ np.eye(4)
+        global_matrix[:, 3][:3] = [float(o) for o in metadata["model_origin_si"].split(",")]
+
+        gprops = tool.Georeference.get_georeference_props()
+        rot = ifcopenshell.util.shape_builder.np_rotation_matrix(radians(-float(gprops.model_project_north)), 4, "Z")
+        local_matrix = rot @ np.eye(4)
+        local_matrix[:, 3][:3] = [float(o) for o in gprops.model_origin_si.split(",")]
+
+        # obj_matrix is typically calculated as:
+        # obj_matrix = np.linalg.inv(local_matrix) @ transformation @ global_matrix
+        identity_blender_matrix = np.linalg.inv(local_matrix) @ global_matrix
+        if np.allclose(new_obj_matrix, identity_blender_matrix, atol=1e-5):
+            link.has_transformation = False
+            transformation = ",".join(map(str, np.eye(4).reshape(-1)))
+        else:
+            transformed_global_matrix = local_matrix @ new_obj_matrix
+            transformation = transformed_global_matrix @ np.linalg.inv(global_matrix)
+            link.has_transformation = True
+            transformation = ",".join(map(str, transformation.reshape(-1)))
+
+        if tool.Ifc.get():
+            reference = tool.Ifc.get().by_id(link.ifc_definition_id)
+            reference[1] = transformation
+        else:
+            link.transformation = transformation
+
     @classmethod
     def append_all_types_from_template(cls, template: str) -> None:
         # TODO refactor
@@ -309,11 +470,17 @@ class Project(bonsai.core.tool.Project):
 
     @classmethod
     def get_linked_models_documents(cls) -> dict[str, ifcopenshell.entity_instance]:
+        """Get linked model documents keyed by resolved absolute filepath (posix form).
+
+        Locations are stored either relative or absolute depending on how the
+        link was created - resolving before keying ensures both forms of the
+        same file match one document.
+        """
         linked_docs = {}
         for doc in tool.Ifc.get().by_type("IfcDocumentInformation"):
             if doc.Scope == "LINKED_MODEL":
                 for reference in tool.Drawing.get_document_references(doc):
-                    linked_docs[Path(reference.Location).as_posix()] = doc
+                    linked_docs[Path(tool.Ifc.resolve_uri(reference.Location)).as_posix()] = doc
                     break
         return linked_docs
 
@@ -321,27 +488,52 @@ class Project(bonsai.core.tool.Project):
     def load_linked_models_from_ifc(cls) -> None:
         links = tool.Project.get_project_props().links
         links.clear()
+        references: list[ifcopenshell.entity_instance] = []
         for doc in tool.Ifc.get().by_type("IfcDocumentInformation"):
             if doc.Scope != "LINKED_MODEL":
                 continue
-            for reference in tool.Drawing.get_document_references(doc):
-                filepath = reference.Location
-                link = links.add()
-                link.name = filepath
-                link.filepath = filepath
-                link.ifc_definition_id = reference.id()
-                link.has_transformation = False
-                if reference[1]:
-                    m = np.fromstring(reference[1], sep=",", dtype=np.float64).reshape(4, 4)
-                    link.has_transformation = not np.allclose(m, np.eye(4))
-                # The selector query used at link time is persisted only in the
-                # sidecar cache JSON; restore it so Reload/Load replay the filter.
+            references.extend(tool.Drawing.get_document_references(doc))
+        location_counts: defaultdict[str, int] = defaultdict(int)
+        for reference in references:
+            location_counts[reference.Location] += 1
+        autoload_indices: list[int] = []
+        for reference in references:
+            filepath = reference.Location
+            link = links.add()
+            link.name = filepath
+            link.filepath = filepath
+            link.ifc_definition_id = reference.id()
+            link.has_transformation = False
+            if reference[1]:
+                m = np.fromstring(reference[1], sep=",", dtype=np.float64).reshape(4, 4)
+                link.has_transformation = not np.allclose(m, np.eye(4))
+            # The selector filter used at link time is persisted per
+            # reference in its Description (IFC4+); restore it so
+            # Reload/Load replay the filter.
+            query, exclude, loaded, display_name = cls.decode_link_filter(getattr(reference, "Description", None))
+            if not query and not exclude and location_counts[filepath] == 1:
+                # Fall back to the legacy sidecar cache JSON where older
+                # versions persisted the query. Only unambiguous: with
+                # several links to one file the shared JSON can't say
+                # which link it belonged to.
                 json_filepath = Path(tool.Ifc.resolve_uri(filepath)).with_suffix(".ifc.cache.json")
                 if json_filepath.exists():
                     try:
-                        link.query = json.loads(json_filepath.read_text()).get("query", "")
+                        query = json.loads(json_filepath.read_text()).get("query", "")
                     except (OSError, json.JSONDecodeError):
                         pass
+            link.query = query
+            link.exclude = exclude
+            link.display_name = display_name
+            if loaded:
+                autoload_indices.append(len(links) - 1)
+
+        # Links that were loaded and visible at save time load automatically.
+        for i in autoload_indices:
+            if not Path(tool.Ifc.resolve_uri(links[i].filepath)).exists():
+                print(f"WARNING: Not auto-loading missing linked model: {links[i].filepath}")
+                continue
+            bpy.ops.bim.load_link(link_index=i)
 
     @classmethod
     def get_project_library_elements(
@@ -858,9 +1050,16 @@ class Project(bonsai.core.tool.Project):
 
             selected_vertices = [obj.matrix_world @ mesh.vertices[vi].co for vi in vert_map]
             for polygon in guid_polygons:
-                selected_tris.append(tuple(vert_map[vi] for vi in polygon.vertices))
                 selected_edges.extend(tuple([vert_map[vi] for vi in e]) for e in polygon.edge_keys)
 
+            # Polygons are not necessarily triangles (e.g. layerset-sliced
+            # meshes contain ngons), so triangles come from the loop triangles.
+            mesh.calc_loop_triangles()
+            polygon_range = range(*slice_.indices(len(mesh.polygons)))
+            for tri in mesh.loop_triangles:
+                if tri.polygon_index in polygon_range:
+                    selected_tris.append(tuple(vert_map[vi] for vi in tri.vertices))
+
             obj["selected_vertices"] = selected_vertices
             obj["selected_edges"] = selected_edges
             obj["selected_tris"] = selected_tris
@@ -897,11 +1096,9 @@ class Project(bonsai.core.tool.Project):
             from bonsai.bim.module.project.data import LinksData
             from bonsai.bim.module.project.decorator import ProjectDecorator
 
-            # Not sure if there's a difference between `instance_matrix` coming from `ray_cast`
-            # and usual `matrix_world`, maybe we can just get it from object always.
-            if instance_matrix is None:
-                instance_matrix = obj.matrix_world
-
+            # `instance_matrix` is the world matrix of the hit collection instance
+            # from `ray_cast` (link empty matrix included). Without it, the root
+            # empty is resolved as the collection's only instance.
             cls.deselect_queried_linked_element()
             cls.set_queried_linked_element(obj, guid, instance_matrix)
             cls.select_linked_element_geom(obj, guid)
@@ -958,7 +1155,7 @@ class Project(bonsai.core.tool.Project):
             ProjectDecorator.install(context)
 
         @classmethod
-        def set_queried_linked_element(cls, obj: bpy.types.Object, guid: str, instance_matrix: Matrix) -> None:
+        def set_queried_linked_element(cls, obj: bpy.types.Object, guid: str, instance_matrix: Matrix | None) -> None:
             props = tool.Project.get_project_props()
             props.queried_obj = obj
             props.queried_obj_root = cls.find_obj_root(obj, instance_matrix)
@@ -977,17 +1174,22 @@ class Project(bonsai.core.tool.Project):
                     del obj[field]
 
         @classmethod
-        def find_obj_root(cls, obj: bpy.types.Object, matrix: Matrix) -> bpy.types.Object | None:
+        def find_obj_root(cls, obj: bpy.types.Object, matrix: Matrix | None) -> bpy.types.Object | None:
             collections = set(obj.users_collection)
-            for o in bpy.data.objects:
-                if (
-                    o.type != "EMPTY"
-                    or o.instance_type != "COLLECTION"
-                    or o.instance_collection not in collections
-                    or not np.allclose(matrix, o.matrix_world, atol=1e-4)
-                ):
-                    continue
-                return o
+            candidates = [
+                o
+                for o in bpy.data.objects
+                if o.type == "EMPTY" and o.instance_type == "COLLECTION" and o.instance_collection in collections
+            ]
+            if matrix is not None:
+                # `matrix` is the instance's world matrix - the instancing
+                # empty's matrix combined with the object's own local matrix
+                # (non-identity for instanced occurrence objects).
+                for o in candidates:
+                    if np.allclose(matrix, np.array(o.matrix_world) @ np.array(obj.matrix_world), atol=1e-4):
+                        return o
+            if len(candidates) == 1:
+                return candidates[0]
 
         class SelectedGeometry(NamedTuple):
             selected_vertices: list[tuple[float, float, float]]
@@ -996,8 +1198,11 @@ class Project(bonsai.core.tool.Project):
 
         @classmethod
         def get_selected_geometry(cls, obj: bpy.types.Object) -> SelectedGeometry:
+            # ID properties are returned as IDPropertyArrays (the whole
+            # property when empty, the items otherwise), which the GPU module
+            # rejects as batch indices - convert to plain tuples.
             return cls.SelectedGeometry(
-                obj["selected_vertices"],
-                obj["selected_edges"],
-                obj["selected_tris"],
+                [tuple(v) for v in obj["selected_vertices"]],
+                [tuple(e) for e in obj["selected_edges"]],
+                [tuple(t) for t in obj["selected_tris"]],
             )

src/bonsai/test/tool/test_project.py

@@ -501,3 +501,72 @@ 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, "")
+
+    def test_display_name_promotes_to_json(self):
+        encoded = subject.encode_link_filter("IfcWall", "", display_name="North Wing")
+        assert encoded.startswith("{")
+        assert subject.decode_link_filter(encoded) == ("IfcWall", "", False, "North Wing")
+
+
+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