fix(web): scope all backend calls to the active repo, not always the first

The root cause of four related issues: `repoRef.current` was never set during
initial server connection — only `switchRepo()` set it. Every backend call
(queries, search, grep, readFile) passed `undefined` as the repo parameter,
so the server's `resolveRepo()` fell back to `repos[0]`.

Changes:
- Expose `setCurrentRepo` from useAppState and call it in `handleServerConnect`
- Use `result.repoInfo.name` (canonical server name) instead of path parsing
- Parse `?project=` URL param during auto-connect, pass it to `connectToServer`
- Update URL with `?project=` on repo switch so F5/bookmarks work
- Pass `projectName` as `repo` in CodeReferencesPanel's `readFile` calls

Closes #139, closes #634, closes #635, closes #636

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

gitnexus-web/src/App.tsx

@@ -45,17 +45,21 @@ const AppContent = () => {
     availableRepos,
     setAvailableRepos,
     switchRepo,
+    setCurrentRepo,
   } = useAppState();
 
   const graphCanvasRef = useRef<GraphCanvasHandle>(null);
 
   const handleServerConnect = useCallback(
     async (result: ConnectResult): Promise<void> => {
-      // Extract project name from repoPath
+      // Use the canonical repo name from the server response so all subsequent
+      // backend calls (queries, search, grep, readFile) scope to this repo.
+      const repoName = result.repoInfo.name;
       const repoPath = result.repoInfo.repoPath ?? result.repoInfo.path;
-      const parts = (repoPath || '').split('/').filter((p) => p && !p.startsWith('.'));
-      const projectName = parts[parts.length - 1] || parts[0] || 'server-project';
+      const projectName =
+        repoName || repoPath?.split('/').filter(Boolean).pop() || 'server-project';
       setProjectName(projectName);
+      setCurrentRepo(projectName);
 
       // Build KnowledgeGraph from server data for visualization
       const graph = createKnowledgeGraph();
@@ -80,10 +84,18 @@ const AppContent = () => {
         console.warn('Failed to initialize agent:', err);
       }
     },
-    [setViewMode, setGraph, setProjectName, initializeAgent, startEmbeddingsWithFallback],
+    [
+      setViewMode,
+      setGraph,
+      setProjectName,
+      setCurrentRepo,
+      initializeAgent,
+      startEmbeddingsWithFallback,
+    ],
   );
 
-  // Auto-connect when ?server query param is present (bookmarkable shortcut)
+  // Auto-connect when ?server query param is present (bookmarkable shortcut).
+  // Also reads ?project= to connect to a specific repo.
   const autoConnectRan = useRef(false);
   useEffect(() => {
     if (autoConnectRan.current) return;
@@ -91,7 +103,10 @@ const AppContent = () => {
     if (!params.has('server')) return;
     autoConnectRan.current = true;
 
-    // Clean the URL so a refresh won't re-trigger
+    const serverUrl = params.get('server') || window.location.origin;
+    const projectParam = params.get('project') || undefined;
+
+    // Clean the URL so a refresh won't re-trigger auto-connect
     const cleanUrl = window.location.pathname + window.location.hash;
     window.history.replaceState(null, '', cleanUrl);
 
@@ -103,36 +118,39 @@ const AppContent = () => {
     });
     setViewMode('loading');
 
-    const serverUrl = params.get('server') || window.location.origin;
-
     const baseUrl = normalizeServerUrl(serverUrl);
 
-    connectToServer(serverUrl, (phase, downloaded, total) => {
-      if (phase === 'validating') {
-        setProgress({
-          phase: 'extracting',
-          percent: 5,
-          message: 'Connecting to server...',
-          detail: 'Validating server',
-        });
-      } else if (phase === 'downloading') {
-        const pct = total ? Math.round((downloaded / total) * 90) + 5 : 50;
-        const mb = (downloaded / (1024 * 1024)).toFixed(1);
-        setProgress({
-          phase: 'extracting',
-          percent: pct,
-          message: 'Downloading graph...',
-          detail: `${mb} MB downloaded`,
-        });
-      } else if (phase === 'extracting') {
-        setProgress({
-          phase: 'extracting',
-          percent: 97,
-          message: 'Processing...',
-          detail: 'Extracting file contents',
-        });
-      }
-    })
+    connectToServer(
+      serverUrl,
+      (phase, downloaded, total) => {
+        if (phase === 'validating') {
+          setProgress({
+            phase: 'extracting',
+            percent: 5,
+            message: 'Connecting to server...',
+            detail: 'Validating server',
+          });
+        } else if (phase === 'downloading') {
+          const pct = total ? Math.round((downloaded / total) * 90) + 5 : 50;
+          const mb = (downloaded / (1024 * 1024)).toFixed(1);
+          setProgress({
+            phase: 'extracting',
+            percent: pct,
+            message: 'Downloading graph...',
+            detail: `${mb} MB downloaded`,
+          });
+        } else if (phase === 'extracting') {
+          setProgress({
+            phase: 'extracting',
+            percent: 97,
+            message: 'Processing...',
+            detail: 'Extracting file contents',
+          });
+        }
+      },
+      undefined,
+      projectParam,
+    )
       .then(async (result) => {
         await handleServerConnect(result);
         setProgress(null);

gitnexus-web/src/components/CodeReferencesPanel.tsx

@@ -54,6 +54,7 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
     clearCodeReferences,
     setSelectedNode,
     codeReferenceFocus,
+    projectName,
   } = useAppState();
 
   const nodeById = useMemo(() => {
@@ -223,10 +224,11 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
     const isWholeFile = selectedIsFile || startLine === undefined;
 
     const options = isWholeFile
-      ? undefined
+      ? { repo: projectName }
       : {
           startLine: Math.max(0, startLine - CONTEXT_LINES),
           endLine: (endLine ?? startLine) + CONTEXT_LINES,
+          repo: projectName,
         };
 
     readFile(selectedFilePath, options)
@@ -251,6 +253,7 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
     selectedNode?.properties?.startLine,
     selectedNode?.properties?.endLine,
     selectedIsFile,
+    projectName,
   ]);
 
   // Scroll to the selected node's startLine after content loads

gitnexus-web/src/hooks/useAppState.tsx

@@ -145,6 +145,7 @@ interface AppState {
   availableRepos: BackendRepo[];
   setAvailableRepos: (repos: BackendRepo[]) => void;
   switchRepo: (repoName: string) => Promise<void>;
+  setCurrentRepo: (repoName: string) => void;
 
   // Worker API (shared across app)
   runQuery: (cypher: string) => Promise<any[]>;
@@ -456,6 +457,10 @@ const AppStateProviderInner = ({ children }: { children: ReactNode }) => {
   // Backend client — direct HTTP calls (no Worker/Comlink)
   const repoRef = useRef<string | undefined>(undefined);
 
+  const setCurrentRepo = useCallback((repoName: string) => {
+    repoRef.current = repoName;
+  }, []);
+
   const runQuery = useCallback(async (cypher: string): Promise<any[]> => {
     return backendRunQuery(cypher, repoRef.current);
   }, []);
@@ -1077,6 +1082,11 @@ const AppStateProviderInner = ({ children }: { children: ReactNode }) => {
         setProjectName(pName);
         repoRef.current = pName;
 
+        // Update URL so F5 / bookmarks open the correct repo
+        const url = new URL(window.location.href);
+        url.searchParams.set('project', pName);
+        window.history.replaceState(null, '', url.toString());
+
         const newGraph = createKnowledgeGraph();
         for (const node of result.nodes) newGraph.addNode(node);
         for (const rel of result.relationships) newGraph.addRelationship(rel);
@@ -1219,6 +1229,7 @@ const AppStateProviderInner = ({ children }: { children: ReactNode }) => {
     availableRepos,
     setAvailableRepos,
     switchRepo,
+    setCurrentRepo,
     runQuery,
     isDatabaseReady,
     // Embedding state and methods