fix: correct issues from merge

src/chunk_manager/base.ts

@@ -100,8 +100,7 @@ export const PREFETCH_PRIORITY_MULTIPLIER = 1e13;
 export const CHUNK_QUEUE_MANAGER_RPC_ID = "ChunkQueueManager";
 export const CHUNK_MANAGER_RPC_ID = "ChunkManager";
 export const CHUNK_SOURCE_INVALIDATE_RPC_ID = "ChunkSource.invalidate";
-export const CHUNK_SOURCE_INVALIDATE_KEYS_RPC_ID =
-  "ChunkSource.invalidateKeys";
+export const CHUNK_SOURCE_INVALIDATE_KEYS_RPC_ID = "ChunkSource.invalidateKeys";
 
 export const REQUEST_CHUNK_STATISTICS_RPC_ID =
   "ChunkQueueManager.requestChunkStatistics";

src/chunk_manager/frontend.ts

@@ -326,7 +326,11 @@ export class ChunkQueueManager extends SharedObject {
 }
 
 function updateChunk(rpc: RPC, x: any) {
-  const source: ChunkSource = rpc.get(x.source);
+  const source = rpc.get(x.source) as ChunkSource | undefined;
+  if (source === undefined) {
+    // Source was removed while chunk update was in flight.
+    return;
+  }
   if (DEBUG_CHUNK_UPDATES) {
     console.log(
       `${Date.now()} Chunk.update received: ` +

src/datasource/catmaid/api.spec.ts

@@ -926,7 +926,18 @@ describe("CatmaidClient skeleton editing methods", () => {
           { nodeId: 201, revisionToken: "2026-03-29T12:04:00Z" },
         ],
       }),
-    ).resolves.toEqual({});
+    ).resolves.toEqual({
+      nodeSourceStateUpdates: [
+        {
+          nodeId: 202,
+          sourceState: testSourceState("2026-03-29T12:08:00Z"),
+        },
+        {
+          nodeId: 201,
+          sourceState: testSourceState("2026-03-29T12:08:00Z"),
+        },
+      ],
+    });
 
     expect(fetchMock).toHaveBeenCalledTimes(1);
     const requestBody = getFetchBody(fetchMock);
@@ -1055,7 +1066,6 @@ describe("CatmaidClient skeleton editing methods", () => {
     const fetchMock = vi.fn().mockResolvedValue({
       newroot: 202,
       skeleton_id: 17,
-      edition_time: "2026-03-29T12:08:00Z",
     });
     (client as any).fetchProjectEndpoint = fetchMock;
 
@@ -1075,7 +1085,9 @@ describe("CatmaidClient skeleton editing methods", () => {
           { nodeId: 201, revisionToken: "2026-03-29T12:04:00Z" },
         ],
       }),
-    ).resolves.toEqual({});
+    ).rejects.toThrow(
+      "CATMAID skeleton/reroot did not return the new root edition_time.",
+    );
     expect(fetchMock).toHaveBeenCalledTimes(1);
   });
 

src/datasource/catmaid/frontend.ts

@@ -482,6 +482,9 @@ export class CatmaidDataSourceProvider implements DataSourceProvider {
         id: "skeletons-chunked",
         default: true,
         subsource: { mesh: multiscaleSource },
+        layerRuntimeStateDisposal: {
+          kind: "spatiallyIndexedSkeleton",
+        },
       },
       {
         id: "skeletons",

src/datasource/catmaid/spatial_skeleton_commands.ts

@@ -450,15 +450,6 @@ function requireCatmaidMergeCommandPayload(payload: object) {
   );
 }
 
-function validateCatmaidNodeDescription(description: string | undefined) {
-  if (description === undefined) return;
-  for (const line of description.split(/\r?\n/)) {
-    if (line.trim().includes(",")) {
-      throw new Error("Node descriptions containing commas are not supported.");
-    }
-  }
-}
-
 function cloneNodeSnapshot(
   node: SpatiallyIndexedSkeletonNode,
 ): SpatiallyIndexedSkeletonNode {
@@ -4314,7 +4305,6 @@ class NodeDescriptionCommand implements SpatialSkeletonCommand {
     nextDescription: string | undefined,
     statusPrefix: string,
   ) {
-    validateCatmaidNodeDescription(nextDescription);
     const { node } = await getResolvedNodeForEdit(
       this.layer,
       this.stableNodeId,

src/datasource/index.ts

@@ -153,6 +153,10 @@ export interface CompleteUrlOptions extends CompleteUrlOptionsBase {
   signal: AbortSignal;
 }
 
+export interface LayerRuntimeStateDisposalRequest {
+  kind: string;
+}
+
 export interface DataSubsourceEntry {
   /**
    * Unique identifier (within the group) for this subsource.  Stored in the JSON state
@@ -182,6 +186,12 @@ export interface DataSubsourceEntry {
    * Specifies whether this associated data source is enabled by default.
    */
   default: boolean;
+
+  /**
+   * Optional layer-owned runtime cleanup requested when this active subsource's
+   * datasource is replaced or cleared.
+   */
+  layerRuntimeStateDisposal?: LayerRuntimeStateDisposalRequest;
 }
 
 export interface ChannelMetadata {

src/layer/index.ts

@@ -38,7 +38,10 @@ import type {
 } from "#src/datasource/index.js";
 import { makeEmptyDataSourceSpecification } from "#src/datasource/index.js";
 import type { DisplayContext, RenderedPanel } from "#src/display_context.js";
-import type { LoadedDataSubsource } from "#src/layer/layer_data_source.js";
+import type {
+  LayerDataSourceChangeRuntimeDisposalContext,
+  LoadedDataSubsource,
+} from "#src/layer/layer_data_source.js";
 import {
   LayerDataSource,
   layerDataSourceSpecificationFromJson,
@@ -431,6 +434,14 @@ export class UserLayer extends RefCounted {
     subsources;
   }
 
+  // Derived classes may override to clear layer-owned runtime state for active
+  // datasources that explicitly request cleanup on source change.
+  disposeLayerRuntimeStateForDataSourceChange(
+    _context: LayerDataSourceChangeRuntimeDisposalContext,
+  ) {
+    return false;
+  }
+
   updateDataSubsourceActivations() {
     function* getDataSubsources(
       this: UserLayer,

src/layer/layer_data_source.ts

@@ -31,6 +31,7 @@ import type {
   DataSourceWithRedirectInfo,
   DataSubsourceEntry,
   DataSubsourceSpecification,
+  LayerRuntimeStateDisposalRequest,
 } from "#src/datasource/index.js";
 import { makeEmptyDataSourceSpecification } from "#src/datasource/index.js";
 import type { UserLayer } from "#src/layer/index.js";
@@ -148,6 +149,7 @@ export class LoadedDataSubsource {
   enabled: boolean;
   activated: RefCounted | undefined = undefined;
   guardValues: any[] = [];
+  renderLayers = new Set<RenderLayer>();
   messages = new MessageList();
   isActiveChanged = new NullarySignal();
   constructor(
@@ -212,9 +214,13 @@ export class LoadedDataSubsource {
 
   addRenderLayer(renderLayer: Owned<RenderLayer>) {
     const activated = this.activated!;
-    activated.registerDisposer(
-      this.loadedDataSource.layer.addRenderLayer(renderLayer),
-    );
+    const removeRenderLayer =
+      this.loadedDataSource.layer.addRenderLayer(renderLayer);
+    this.renderLayers.add(renderLayer);
+    activated.registerDisposer(() => {
+      this.renderLayers.delete(renderLayer);
+      removeRenderLayer();
+    });
     activated.registerDisposer(this.messages.addChild(renderLayer.messages));
   }
 
@@ -301,6 +307,16 @@ export class LoadedLayerDataSource extends RefCounted {
   }
 }
 
+export type LayerDataSourceChangeReason = "replace" | "clear";
+
+export interface LayerDataSourceChangeRuntimeDisposalContext {
+  request: LayerRuntimeStateDisposalRequest;
+  reason: LayerDataSourceChangeReason;
+  layerDataSource: LayerDataSource;
+  loadedDataSource: LoadedLayerDataSource;
+  loadedSubsource: LoadedDataSubsource;
+}
+
 export type LayerDataSourceLoadState =
   | {
       error: Error;
@@ -368,10 +384,36 @@ export class LayerDataSource extends RefCounted {
     return this.loadState_;
   }
 
+  private disposeRuntimeStateForDataSourceChange(
+    reason: LayerDataSourceChangeReason,
+  ) {
+    const { loadState } = this;
+    if (loadState === undefined || loadState.error !== undefined) return false;
+    const handledRequestKinds = new Set<string>();
+    let changed = false;
+    for (const loadedSubsource of loadState.subsources) {
+      if (loadedSubsource.activated === undefined) continue;
+      const request = loadedSubsource.subsourceEntry.layerRuntimeStateDisposal;
+      if (request === undefined) continue;
+      if (handledRequestKinds.has(request.kind)) continue;
+      handledRequestKinds.add(request.kind);
+      changed =
+        this.layer.disposeLayerRuntimeStateForDataSourceChange({
+          request,
+          reason,
+          layerDataSource: this,
+          loadedDataSource: loadState,
+          loadedSubsource,
+        }) || changed;
+    }
+    return changed;
+  }
+
   set spec(spec: DataSourceSpecification) {
     const { layer } = this;
     this.messages.clearMessages();
     if (spec.url.length === 0) {
+      this.disposeRuntimeStateForDataSourceChange("clear");
       if (layer.dataSources.length !== 1) {
         const index = layer.dataSources.indexOf(this);
         if (index !== -1) {
@@ -395,6 +437,7 @@ export class LayerDataSource extends RefCounted {
       disposableOnce(layer.markLoading()),
     );
     if (this.refCounted_ !== undefined) {
+      this.disposeRuntimeStateForDataSourceChange("replace");
       this.refCounted_.dispose();
       this.loadState_ = undefined;
     }

src/layer/segmentation/index.ts

@@ -42,7 +42,10 @@ import {
   registerVolumeLayerType,
   UserLayer,
 } from "#src/layer/index.js";
-import type { LoadedDataSubsource } from "#src/layer/layer_data_source.js";
+import type {
+  LayerDataSourceChangeRuntimeDisposalContext,
+  LoadedDataSubsource,
+} from "#src/layer/layer_data_source.js";
 import { layerDataSourceSpecificationFromJson } from "#src/layer/layer_data_source.js";
 import * as json_keys from "#src/layer/segmentation/json_keys.js";
 import { registerLayerControls } from "#src/layer/segmentation/layer_controls.js";
@@ -104,6 +107,7 @@ import {
   SKELETON_GO_ROOT,
   SKELETON_GO_UNFINISHED,
   SKELETON_REDO,
+  SKELETON_TOGGLE_HIDDEN,
   SKELETON_UNDO,
 } from "#src/skeleton/actions.js";
 import type {
@@ -812,6 +816,9 @@ function copyOptionalSpatialSkeletonPosition(
   return new Float32Array(Array.from(value, Number));
 }
 
+const SPATIALLY_INDEXED_SKELETON_RUNTIME_DISPOSAL_KIND =
+  "spatiallyIndexedSkeleton";
+
 const Base = UserLayerWithAnnotationsMixin(UserLayer);
 export class SegmentationUserLayer extends Base {
   sliceViewRenderScaleHistogram = new RenderScaleHistogram();
@@ -1095,6 +1102,8 @@ export class SegmentationUserLayer extends Base {
     x === undefined ? undefined : parseUint64(x),
   );
 
+  private savedHiddenObjectAlpha: number | undefined;
+
   constructor(managedLayer: Borrowed<ManagedUserLayer>) {
     super(managedLayer);
     this.codeVisible.changed.add(this.specificationChanged.dispatch);
@@ -1597,6 +1606,31 @@ export class SegmentationUserLayer extends Base {
     this.spatialSkeletonState.markNodeDataChanged(options);
   }
 
+  disposeLayerRuntimeStateForDataSourceChange(
+    context: LayerDataSourceChangeRuntimeDisposalContext,
+  ) {
+    if (
+      context.request.kind !== SPATIALLY_INDEXED_SKELETON_RUNTIME_DISPOSAL_KIND
+    ) {
+      return super.disposeLayerRuntimeStateForDataSourceChange(context);
+    }
+    let changed = false;
+    const spatialSkeletonLayers = new Set<SpatiallyIndexedSkeletonLayer>();
+    for (const renderLayer of context.loadedSubsource.renderLayers) {
+      if (
+        renderLayer instanceof PerspectiveViewSpatiallyIndexedSkeletonLayer ||
+        renderLayer instanceof SliceViewPanelSpatiallyIndexedSkeletonLayer
+      ) {
+        spatialSkeletonLayers.add(renderLayer.base);
+      }
+    }
+    for (const spatialSkeletonLayer of spatialSkeletonLayers) {
+      changed = spatialSkeletonLayer.disposeRuntimeState() || changed;
+    }
+    changed = this.spatialSkeletonState.clearRuntimeState() || changed;
+    return changed;
+  }
+
   activateDataSubsources(subsources: Iterable<LoadedDataSubsource>) {
     const updatedSegmentPropertyMaps: SegmentPropertyMap[] = [];
     const isGroupRoot =
@@ -2100,6 +2134,17 @@ export class SegmentationUserLayer extends Base {
         }
         break;
       }
+      case SKELETON_TOGGLE_HIDDEN: {
+        const { hiddenObjectAlpha } = this.displayState;
+        if (this.savedHiddenObjectAlpha !== undefined) {
+          hiddenObjectAlpha.value = this.savedHiddenObjectAlpha;
+          this.savedHiddenObjectAlpha = undefined;
+        } else {
+          this.savedHiddenObjectAlpha = hiddenObjectAlpha.value;
+          hiddenObjectAlpha.value = 0;
+        }
+        break;
+      }
       case SKELETON_GO_ROOT:
       case SKELETON_GO_BRANCH_START:
       case SKELETON_GO_BRANCH_END:
@@ -2676,13 +2721,11 @@ export class SegmentationUserLayer extends Base {
             ? svg_circle
             : nodeType === undefined
               ? svg_circle
-              : nodeType === undefined
-                ? svg_circle
-                : SPATIAL_SKELETON_NODE_TYPE_ICONS[nodeType],
-        title: nodeTypeIconTitle,
-        clickable: false,
-      }),
-    );
+              : SPATIAL_SKELETON_NODE_TYPE_ICONS[nodeType],
+      title: nodeTypeIconTitle,
+      clickable: false,
+    });
+    icon.appendChild(nodeTypeIcon);
     summaryRow.appendChild(icon);
 
     const skeletonDisplayTransform =

src/skeleton/actions.ts

@@ -44,3 +44,6 @@ export const SKELETON_ENTER_CREATE = "skeleton-enter-create";
 export const SKELETON_PIN_NODE = "skeleton-pin-node";
 export const SKELETON_ENTER_DELETE_MODE = "skeleton-enter-delete-mode";
 export const SKELETON_CLEAR_SELECTION = "skeleton-clear-node-selection";
+
+// --- Display toggles ---
+export const SKELETON_TOGGLE_HIDDEN = "skeleton-toggle-hidden";

src/skeleton/command_history.ts

@@ -77,6 +77,10 @@ export class SpatialSkeletonCommandMappings {
   private nodeIdMappings = new Map<number, number>();
   private segmentIdMappings = new Map<number, number>();
 
+  get empty() {
+    return this.nodeIdMappings.size === 0 && this.segmentIdMappings.size === 0;
+  }
+
   clear() {
     this.nodeIdMappings.clear();
     this.segmentIdMappings.clear();
@@ -241,10 +245,15 @@ export class SpatialSkeletonCommandHistory extends RefCounted {
   }
 
   clear() {
+    const changed =
+      this.undoEntries.length !== 0 ||
+      this.redoEntries.length !== 0 ||
+      !this.mappings.empty;
     this.undoEntries = [];
     this.redoEntries = [];
     this.mappings.clear();
     this.updateState();
+    return changed;
   }
 
   setSource(source: unknown) {