fix(web): LadybugDB getAllRows, loadServerGraph, BM25, highlight clearing

.husky/pre-commit

@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+# Pre-commit hook (husky): typecheck + unit tests for both packages.
+# Mirrors CI checks from ci-quality.yml and ci-tests.yml.
+# Skip with: git commit --no-verify
+#
+# CI coverage:
+#   quality / typecheck      → tsc --noEmit in gitnexus/
+#   quality / typecheck-web  → tsc -b --noEmit in gitnexus-web/
+#   tests / ubuntu+coverage  → vitest run in gitnexus/ (all projects)
+#   e2e / chromium           → playwright (requires servers — skipped)
+
+ROOT="$(git rev-parse --show-toplevel)"
+
+WEB_CHANGED=$(git diff --cached --name-only -- 'gitnexus-web/' | head -1)
+CLI_CHANGED=$(git diff --cached --name-only -- 'gitnexus/' | head -1)
+
+if [ -n "$WEB_CHANGED" ]; then
+  echo "pre-commit: typechecking gitnexus-web (tsc -b)..."
+  cd "$ROOT/gitnexus-web" && npx tsc -b --noEmit
+
+  echo "pre-commit: running gitnexus-web unit tests..."
+  npx vitest run --reporter=dot
+fi
+
+if [ -n "$CLI_CHANGED" ]; then
+  echo "pre-commit: typechecking gitnexus..."
+  cd "$ROOT/gitnexus" && npx tsc --noEmit
+
+  echo "pre-commit: running gitnexus unit tests (default project)..."
+  npx vitest run --project default --reporter=dot
+fi
+
+echo "pre-commit: all checks passed"

gitnexus-web/src/App.tsx

@@ -27,7 +27,6 @@ const AppContent = () => {
     isRightPanelOpen,
     runPipeline,
     runPipelineFromFiles,
-    hydrateServerGraph,
     isSettingsPanelOpen,
     setSettingsPanelOpen,
     isHelpDialogBoxOpen,
@@ -44,7 +43,7 @@ const AppContent = () => {
     availableRepos,
     setAvailableRepos,
     switchRepo,
-    hydrateWorkerFromServer,
+    loadServerGraph,
     graph
   } = useAppState();
 
@@ -138,13 +137,13 @@ const AppContent = () => {
     }
   }, [setViewMode, setGraph, setFileContents, setProgress, setProjectName, runPipelineFromFiles, startEmbeddings, initializeAgent]);
 
-  const handleServerConnect = useCallback(async (result: ConnectToServerResult) => {
+  const handleServerConnect = useCallback((result: ConnectToServerResult): Promise<void> => {
     // Extract project name from repoPath
     const repoPath = result.repoInfo.repoPath;
     const projectName = repoPath.split('/').pop() || 'server-project';
     setProjectName(projectName);
 
-    // Build KnowledgeGraph from server data (bypasses WASM pipeline entirely)
+    // Build KnowledgeGraph from server data for visualization
     const graph = createKnowledgeGraph();
     for (const node of result.nodes) {
       graph.addNode(node);
@@ -161,38 +160,33 @@ const AppContent = () => {
     }
     setFileContents(fileMap);
 
-    try {
-      await hydrateServerGraph(result);
-
-      // Transition directly to exploring view
-      setViewMode('exploring');
-    } finally {
-      setProgress(null);
-    }
-
-    // Hydrate the worker-side DB (LadybugDB + BM25) so Query/Processes/embeddings work
-    hydrateWorkerFromServer(result.nodes, result.relationships, result.fileContents).then(() => {
-      // Initialize agent if LLM is configured
-      if (getActiveProviderConfig()) {
-        initializeAgent(projectName);
-      }
+    // Transition directly to exploring view
+    setViewMode('exploring');
 
-      // Auto-start embeddings (now that LadybugDB is ready)
-      startEmbeddings().catch((err) => {
-        if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
-          startEmbeddings('wasm').catch(console.warn);
-        } else {
-          console.warn('Embeddings auto-start failed:', err);
+    // Load graph into LadybugDB (in-browser WASM database) for Nexus AI queries,
+    // then initialize agent once the database is ready
+    const loadGraphPromise = loadServerGraph(result.nodes, result.relationships, result.fileContents)
+      .then(() => {
+        if (getActiveProviderConfig()) {
+          return initializeAgent(projectName);
         }
+      })
+      .then(() => {
+        startEmbeddings().catch((err) => {
+          if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
+            startEmbeddings('wasm').catch(console.warn);
+          } else {
+            console.warn('Embeddings auto-start failed:', err);
+          }
+        });
+      })
+      .catch((err) => {
+        console.warn('Failed to load graph into LadybugDB:', err);
+        // Agent won't work but graph visualization still does
       });
-    }).catch((err) => {
-      console.warn('Worker hydration failed (non-fatal):', err);
-      // Still initialize agent even if hydration fails
-      if (getActiveProviderConfig()) {
-        initializeAgent(projectName);
-      }
-    });
-  }, [setViewMode, setGraph, setFileContents, setProjectName, setProgress, initializeAgent, startEmbeddings, hydrateServerGraph, hydrateWorkerFromServer]);
+
+    return loadGraphPromise;
+  }, [setViewMode, setGraph, setFileContents, setProjectName, loadServerGraph, initializeAgent, startEmbeddings]);
 
   // Auto-connect when ?server query param is present (bookmarkable shortcut)
   const autoConnectRan = useRef(false);
@@ -225,15 +219,11 @@ const AppContent = () => {
       }
     }).then(async (result) => {
       await handleServerConnect(result);
-
-      // Store server URL and fetch available repos for the repo switcher
+      setProgress(null);
       setServerBaseUrl(baseUrl);
-      try {
-        const repos = await fetchRepos(baseUrl);
-        setAvailableRepos(repos);
-      } catch (e) {
-        console.warn('Failed to fetch repo list:', e);
-      }
+      fetchRepos(baseUrl)
+        .then((repos) => setAvailableRepos(repos))
+        .catch((e) => console.warn('Failed to fetch repo list:', e));
     }).catch((err) => {
       console.error('Auto-connect failed:', err);
       setProgress({
@@ -268,15 +258,13 @@ const AppContent = () => {
         onGitClone={handleGitClone}
         onServerConnect={async (result, serverUrl) => {
           await handleServerConnect(result);
+          setProgress(null);
           if (serverUrl) {
             const baseUrl = normalizeServerUrl(serverUrl);
             setServerBaseUrl(baseUrl);
-            try {
-              const repos = await fetchRepos(baseUrl);
-              setAvailableRepos(repos);
-            } catch (e) {
-              console.warn('Failed to fetch repo list:', e);
-            }
+            fetchRepos(baseUrl)
+              .then((repos) => setAvailableRepos(repos))
+              .catch((e) => console.warn('Failed to fetch repo list:', e));
           }
         }}
       />

gitnexus-web/src/components/GraphCanvas.tsx

@@ -26,6 +26,9 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
     blastRadiusNodeIds,
     isAIHighlightsEnabled,
     toggleAIHighlights,
+    clearAIToolHighlights,
+    clearAICitationHighlights,
+    clearBlastRadius,
     animatedNodes,
   } = useAppState();
   const [hoveredNodeName, setHoveredNodeName] = useState<string | null>(null);
@@ -305,9 +308,13 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
       <div className="absolute top-4 right-4 z-20">
         <button
           onClick={() => {
-            // If turning off, also clear process highlights
             if (isAIHighlightsEnabled) {
-              setHighlightedNodeIds(new Set());
+              // Turning off — clear AI highlights and selection (preserve user query highlights)
+              clearAIToolHighlights();
+              clearAICitationHighlights();
+              clearBlastRadius();
+              setSelectedNode(null);
+              setSigmaSelectedNode(null);
             }
             toggleAIHighlights();
           }}

gitnexus-web/src/hooks/useAppState.tsx

@@ -1,6 +1,6 @@
 import { createContext, useContext, useState, useCallback, useRef, useEffect, ReactNode } from 'react';
 import * as Comlink from 'comlink';
-import { KnowledgeGraph, GraphNode, NodeLabel } from '../core/graph/types';
+import { KnowledgeGraph, GraphNode, GraphRelationship, NodeLabel } from '../core/graph/types';
 import { PipelineProgress, PipelineResult, deserializePipelineResult } from '../types/pipeline';
 import { createKnowledgeGraph } from '../core/graph/graph';
 import { DEFAULT_VISIBLE_LABELS } from '../lib/constants';
@@ -95,6 +95,7 @@ interface AppState {
   isAIHighlightsEnabled: boolean;
   toggleAIHighlights: () => void;
   clearAIToolHighlights: () => void;
+  clearAICitationHighlights: () => void;
   clearBlastRadius: () => void;
   queryResult: QueryResult | null;
   setQueryResult: (result: QueryResult | null) => void;
@@ -123,10 +124,9 @@ interface AppState {
   // Worker API (shared across app)
   runPipeline: (file: File, onProgress: (p: PipelineProgress) => void, clusteringConfig?: ProviderConfig) => Promise<PipelineResult>;
   runPipelineFromFiles: (files: FileEntry[], onProgress: (p: PipelineProgress) => void, clusteringConfig?: ProviderConfig) => Promise<PipelineResult>;
-  hydrateServerGraph: (result: ConnectToServerResult) => Promise<void>;
   runQuery: (cypher: string) => Promise<any[]>;
   isDatabaseReady: () => Promise<boolean>;
-  hydrateWorkerFromServer: (nodes: any[], relationships: any[], fileContents: Record<string, string>) => Promise<void>;
+  loadServerGraph: (nodes: GraphNode[], relationships: GraphRelationship[], fileContents: Record<string, string>) => Promise<void>;
 
   // Embedding state
   embeddingStatus: EmbeddingStatus;
@@ -229,6 +229,10 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     setAIToolHighlightedNodeIds(new Set());
   }, []);
 
+  const clearAICitationHighlights = useCallback(() => {
+    setAICitationHighlightedNodeIds(new Set());
+  }, []);
+
   const clearBlastRadius = useCallback(() => {
     setBlastRadiusNodeIds(new Set());
   }, []);
@@ -471,16 +475,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     return deserializePipelineResult(serializedResult, createKnowledgeGraph);
   }, []);
 
-  const hydrateServerGraph = useCallback(async (result: ConnectToServerResult): Promise<void> => {
-    const api = apiRef.current;
-    if (!api) throw new Error('Worker not initialized');
-    await api.hydrateServerGraph({
-      nodes: result.nodes,
-      relationships: result.relationships,
-      fileContents: result.fileContents,
-    });
-  }, []);
-
   const runQuery = useCallback(async (cypher: string): Promise<any[]> => {
     const api = apiRef.current;
     if (!api) throw new Error('Worker not initialized');
@@ -497,14 +491,14 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     }
   }, []);
 
-  const hydrateWorkerFromServer = useCallback(async (
-    nodes: any[],
-    relationships: any[],
+  const loadServerGraph = useCallback(async (
+    nodes: GraphNode[],
+    relationships: GraphRelationship[],
     fileContents: Record<string, string>
   ): Promise<void> => {
     const api = apiRef.current;
     if (!api) throw new Error('Worker not initialized');
-    await api.hydrateFromServerData(nodes, relationships, fileContents);
+    await api.loadServerGraph(nodes, relationships, fileContents);
   }, []);
 
   // Embedding methods
@@ -1004,10 +998,13 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     setProgress({ phase: 'extracting', percent: 0, message: 'Switching repository...', detail: `Loading ${repoName}` });
     setViewMode('loading');
 
+    setIsAgentReady(false);
+
     // Clear stale graph state from previous repo (highlights, selections, blast radius)
     // Without this, sigma reducers dim ALL nodes/edges because old node IDs don't match
     setHighlightedNodeIds(new Set());
     clearAIToolHighlights();
+    clearAICitationHighlights();
     clearBlastRadius();
     setSelectedNode(null);
     setQueryResult(null);
@@ -1042,37 +1039,41 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
       for (const [p, c] of Object.entries(result.fileContents)) fileMap.set(p, c);
       setFileContents(fileMap);
 
-      await hydrateServerGraph(result);
-
-      setViewMode('exploring');
-      setProgress(null);
-
-      // Hydrate the worker-side DB (LadybugDB + BM25) so Query/Processes/embeddings work
-      hydrateWorkerFromServer(result.nodes, result.relationships, result.fileContents).then(() => {
-        if (getActiveProviderConfig()) initializeAgent(pName);
-
+      // Load graph into LadybugDB for Nexus AI queries, then init agent
+      try {
+        await loadServerGraph(result.nodes, result.relationships, result.fileContents);
+        if (getActiveProviderConfig()) {
+          await initializeAgent(pName);
+        }
+        setViewMode('exploring');
         startEmbeddings().catch((err) => {
           if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
             startEmbeddings('wasm').catch(console.warn);
           } else {
             console.warn('Embeddings auto-start failed:', err);
           }
         });
-      }).catch((err) => {
-        console.warn('Worker hydration failed (non-fatal):', err);
-        // Still initialize agent even if hydration fails
-        if (getActiveProviderConfig()) initializeAgent(pName);
-      });
+        setProgress(null);
+      } catch (err) {
+        console.warn('Failed to load graph into LadybugDB:', err);
+        setIsAgentReady(false);
+        await apiRef.current?.disposeAgent();
+        setAgentError('Failed to load graph into LadybugDB');
+        setViewMode('exploring');
+        setProgress(null);
+      }
     } catch (err) {
       console.error('Repo switch failed:', err);
       setProgress({
         phase: 'error', percent: 0,
         message: 'Failed to switch repository',
         detail: err instanceof Error ? err.message : 'Unknown error',
       });
+      setIsAgentReady(false);
+      await apiRef.current?.disposeAgent();
       setTimeout(() => { setViewMode('exploring'); setProgress(null); }, 3000);
     }
-  }, [serverBaseUrl, setProgress, setViewMode, setProjectName, setGraph, setFileContents, initializeAgent, startEmbeddings, hydrateServerGraph, hydrateWorkerFromServer, setHighlightedNodeIds, clearAIToolHighlights, clearBlastRadius, setSelectedNode, setQueryResult, setCodeReferences, setCodePanelOpen, setCodeReferenceFocus]);
+  }, [serverBaseUrl, setProgress, setViewMode, setProjectName, setGraph, setFileContents, loadServerGraph, initializeAgent, startEmbeddings, setHighlightedNodeIds, clearAIToolHighlights, clearAICitationHighlights, clearBlastRadius, setSelectedNode, setQueryResult, setCodeReferences, setCodePanelOpen, setCodeReferenceFocus]);
 
   const removeCodeReference = useCallback((id: string) => {
     setCodeReferences(prev => {
@@ -1155,6 +1156,7 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     isAIHighlightsEnabled,
     toggleAIHighlights,
     clearAIToolHighlights,
+    clearAICitationHighlights,
     clearBlastRadius,
     queryResult,
     setQueryResult,
@@ -1175,10 +1177,9 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     switchRepo,
     runPipeline,
     runPipelineFromFiles,
-    hydrateServerGraph,
     runQuery,
     isDatabaseReady,
-    hydrateWorkerFromServer,
+    loadServerGraph,
     // Embedding state and methods
     embeddingStatus,
     embeddingProgress,