Add workspace file browser and OpenAlex citation search

Workspace browser:
- The left panel gains a Project/Workspace toggle; the Workspace view
  browses the agent scratch space (claude-workspace/, never synced)
- Open/edit workspace text files in the editor with debounced auto-save
  (flushed on tab switch); binaries open with the system default app
- Import to Project copies a workspace file/folder into the project root
  where the sync bridge picks it up and creates it on Overleaf
  (collision-safe: falls back to a -imported suffix)
- New file/folder, rename, delete, reveal in Finder, drag-drop into the
  workspace, 5s auto-refresh while visible

OpenAlex search (MCP):
- New search_openalex tool: broad OpenAlex coverage with an explicit
  citation-authority policy — BibTeX is cross-checked against Semantic
  Scholar (by DOI, then by exact title, since OpenAlex DOIs can point at
  mirrors); entries not found on S2 are flagged "OpenAlex only" with
  instructions to verify via web search before citing
- Tool description, agent guide, permission allowlist, and README updated

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

3 files changed, 386 insertions, 27 deletions

diff --git a/src/renderer/src/App.css b/src/renderer/src/App.css
index 0db81f8..69f0139 100644
--- a/src/renderer/src/App.css
+++ b/src/renderer/src/App.css
@@ -486,6 +486,56 @@ html, body, #root {
   border-bottom: 1px solid var(--border);
 }
 
+/* Project / Workspace view toggle */
+.file-tree-tabs {
+  padding: 6px 8px;
+  gap: 4px;
+  justify-content: flex-start;
+}
+.file-tree-tab {
+  flex: 1;
+  padding: 4px 8px;
+  font-size: 11px;
+  font-weight: 600;
+  letter-spacing: 0.5px;
+  text-transform: uppercase;
+  color: var(--text-muted);
+  background: none;
+  border: none;
+  border-radius: var(--radius);
+  cursor: pointer;
+  font-family: var(--font-sans);
+}
+.file-tree-tab:hover {
+  background: var(--bg-hover);
+  color: var(--text-primary);
+}
+.file-tree-tab.active {
+  background: var(--bg-active);
+  color: var(--text-primary);
+}
+
+.file-tree-ws-toolbar {
+  display: flex;
+  gap: 4px;
+  padding: 6px 8px;
+  border-bottom: 1px solid var(--border);
+}
+.file-tree-ws-btn {
+  padding: 3px 8px;
+  font-size: 11px;
+  color: var(--text-secondary);
+  background: var(--bg-tertiary);
+  border: none;
+  border-radius: var(--radius);
+  cursor: pointer;
+  font-family: var(--font-sans);
+}
+.file-tree-ws-btn:hover {
+  background: var(--bg-hover);
+  color: var(--text-primary);
+}
+
 .file-tree-action {
   width: 22px;
   height: 22px;
diff --git a/src/renderer/src/components/Editor.tsx b/src/renderer/src/components/Editor.tsx
index 2afdc0e..14373d1 100644
--- a/src/renderer/src/components/Editor.tsx
+++ b/src/renderer/src/components/Editor.tsx
@@ -88,6 +88,7 @@ export default function Editor() {
   const docSyncRef = useRef<OverleafDocSync | null>(null)
 
   const cursorThrottleRef = useRef<ReturnType<typeof setTimeout> | null>(null)
+  const wsSaveTimerRef = useRef<ReturnType<typeof setTimeout> | null>(null)
   const [editorFontSize, setEditorFontSize] = useState(13.5)
 
   // Add comment state
@@ -181,6 +182,19 @@ export default function Editor() {
         const docId = pathDocMap[activeTab]
         if (docId) {
           window.api.syncContentChanged(docId, newContent)
+        } else if (activeTab.startsWith('claude-workspace/')) {
+          // Workspace files live only on disk — debounced auto-save
+          const dir = useAppStore.getState().syncDir
+          if (dir) {
+            if (wsSaveTimerRef.current) clearTimeout(wsSaveTimerRef.current)
+            const tab = activeTab
+            wsSaveTimerRef.current = setTimeout(() => {
+              wsSaveTimerRef.current = null
+              window.api.writeFile(`${dir}/${tab}`, newContent)
+                .then(() => useAppStore.getState().markModified(tab, false))
+                .catch(() => useAppStore.getState().setStatusMessage(`Failed to save ${tab}`))
+            }, 500)
+          }
         }
       }
       if (update.selectionSet) {
@@ -301,6 +315,18 @@ export default function Editor() {
     }
 
     return () => {
+      // Flush a pending workspace save so switching tabs never loses edits
+      if (wsSaveTimerRef.current && activeTab?.startsWith('claude-workspace/')) {
+        clearTimeout(wsSaveTimerRef.current)
+        wsSaveTimerRef.current = null
+        const dir = useAppStore.getState().syncDir
+        const content = useAppStore.getState().fileContents[activeTab]
+        if (dir && content !== undefined) {
+          window.api.writeFile(`${dir}/${activeTab}`, content)
+            .then(() => useAppStore.getState().markModified(activeTab, false))
+            .catch(() => {})
+        }
+      }
       if (docSyncRef.current) {
         const docId = pathDocMap[activeTab!]
         if (docId) {
diff --git a/src/renderer/src/components/FileTree.tsx b/src/renderer/src/components/FileTree.tsx
index 1b9ce5e..5486f20 100644
--- a/src/renderer/src/components/FileTree.tsx
+++ b/src/renderer/src/components/FileTree.tsx
@@ -4,10 +4,24 @@
 import { useState, useCallback, useEffect, useRef } from 'react'
 import { useAppStore, type FileNode } from '../stores/appStore'
 
+const BINARY_EXTS = new Set(['pdf', 'png', 'jpg', 'jpeg', 'gif', 'svg', 'eps', 'zip', 'tiff', 'bmp'])
+
 interface ContextMenuState {
   x: number
   y: number
   node: FileNode
+  view: 'project' | 'workspace'
+}
+
+function fileIcon(node: FileNode, expanded: boolean): string {
+  if (node.isDir) return expanded ? '📂' : '📁'
+  const ext = node.name.split('.').pop()?.toLowerCase() ?? ''
+  return ext === 'tex' ? '📄'
+    : ext === 'bib' ? '📚'
+    : ext === 'pdf' ? '📕'
+    : ext === 'png' || ext === 'jpg' || ext === 'jpeg' ? '🖼️'
+    : ext === 'py' || ext === 'sh' ? '⚙️'
+    : '📝'
 }
 
 function FileTreeNode({
@@ -20,7 +34,7 @@ function FileTreeNode({
   onContextMenu: (e: React.MouseEvent, node: FileNode) => void
 }) {
   const [expanded, setExpanded] = useState(depth < 2)
-  const { activeTab, openFile, setFileContent, setStatusMessage, mainDocument, docPathMap } = useAppStore()
+  const { activeTab, openFile, setFileContent, setStatusMessage, mainDocument } = useAppStore()
   const isActive = activeTab === node.path
   const isMainDoc = node.docId && mainDocument === node.docId
 
@@ -70,15 +84,6 @@ function FileTreeNode({
     }
   }, [node, expanded, openFile, setFileContent, setStatusMessage])
 
-  const ext = node.name.split('.').pop()?.toLowerCase() ?? ''
-  const icon = node.isDir
-    ? expanded ? '📂' : '📁'
-    : ext === 'tex' ? '📄'
-    : ext === 'bib' ? '📚'
-    : ext === 'pdf' ? '📕'
-    : ext === 'png' || ext === 'jpg' ? '🖼️'
-    : '📝'
-
   return (
     <div>
       <div
@@ -87,7 +92,7 @@ function FileTreeNode({
         onClick={handleClick}
         onContextMenu={(e) => onContextMenu(e, node)}
       >
-        <span className="file-icon">{icon}</span>
+        <span className="file-icon">{fileIcon(node, expanded)}</span>
         <span className="file-name">
           {node.name}
           {isMainDoc && <span className="main-doc-badge">main</span>}
@@ -100,11 +105,84 @@ function FileTreeNode({
   )
 }
 
+/** Workspace (agent scratch space) node — files live on disk, not on Overleaf */
+function WorkspaceNode({
+  node,
+  depth,
+  onContextMenu
+}: {
+  node: FileNode
+  depth: number
+  onContextMenu: (e: React.MouseEvent, node: FileNode) => void
+}) {
+  const [expanded, setExpanded] = useState(depth < 2)
+  const { activeTab, openFile, setFileContent, setStatusMessage, syncDir } = useAppStore()
+  const isActive = activeTab === node.path
+
+  const handleClick = useCallback(async () => {
+    if (node.isDir) {
+      setExpanded(!expanded)
+      return
+    }
+    const abs = `${syncDir}/${node.path}`
+    const ext = node.name.split('.').pop()?.toLowerCase() ?? ''
+    if (BINARY_EXTS.has(ext)) {
+      // Open binaries with the system default app
+      window.api.openPath(abs)
+      return
+    }
+    try {
+      const content = await window.api.readFile(abs)
+      setFileContent(node.path, content)
+      openFile(node.path, node.name)
+    } catch {
+      setStatusMessage(`Failed to open ${node.name}`)
+    }
+  }, [node, expanded, syncDir, openFile, setFileContent, setStatusMessage])
+
+  return (
+    <div>
+      <div
+        className={`file-tree-item ${isActive ? 'active' : ''}`}
+        style={{ paddingLeft: depth * 16 + 8 }}
+        onClick={handleClick}
+        onContextMenu={(e) => onContextMenu(e, node)}
+      >
+        <span className="file-icon">{fileIcon(node, expanded)}</span>
+        <span className="file-name">{node.name}</span>
+      </div>
+      {node.isDir && expanded && node.children?.map((child) => (
+        <WorkspaceNode key={child.path} node={child} depth={depth + 1} onContextMenu={onContextMenu} />
+      ))}
+    </div>
+  )
+}
+
 export default function FileTree() {
-  const { files } = useAppStore()
+  const { files, syncDir } = useAppStore()
+  const [view, setView] = useState<'project' | 'workspace'>('project')
+  const [wsNodes, setWsNodes] = useState<FileNode[]>([])
   const [ctxMenu, setCtxMenu] = useState<ContextMenuState | null>(null)
   const menuRef = useRef<HTMLDivElement>(null)
 
+  const workspaceRoot = syncDir ? `${syncDir}/claude-workspace` : ''
+
+  const loadWorkspace = useCallback(async () => {
+    if (!workspaceRoot) return
+    try {
+      const nodes = await window.api.listDirTree(workspaceRoot, 'claude-workspace/')
+      setWsNodes(nodes as FileNode[])
+    } catch { /* workspace may not exist yet */ }
+  }, [workspaceRoot])
+
+  // Refresh workspace on switch + poll while visible (agents write here)
+  useEffect(() => {
+    if (view !== 'workspace') return
+    loadWorkspace()
+    const timer = setInterval(loadWorkspace, 5000)
+    return () => clearInterval(timer)
+  }, [view, loadWorkspace])
+
   // Close context menu on outside click or escape
   useEffect(() => {
     if (!ctxMenu) return
@@ -127,11 +205,13 @@ export default function FileTree() {
   const handleContextMenu = useCallback((e: React.MouseEvent, node: FileNode) => {
     e.preventDefault()
     e.stopPropagation()
-    setCtxMenu({ x: e.clientX, y: e.clientY, node })
-  }, [])
+    setCtxMenu({ x: e.clientX, y: e.clientY, node, view })
+  }, [view])
 
   const closeMenu = () => setCtxMenu(null)
 
+  // ── Project view actions (Overleaf entities) ──
+
   const handleSetMainDoc = () => {
     if (!ctxMenu) return
     const node = ctxMenu.node
@@ -258,6 +338,103 @@ export default function FileTree() {
     closeMenu()
   }
 
+  // ── Workspace view actions (disk files under claude-workspace/) ──
+
+  const wsAbs = (node: FileNode) => `${syncDir}/${node.path}`
+
+  /** Copy a workspace file/folder into the project root — the sync bridge
+      detects it and creates it on Overleaf. */
+  const handleImportToProject = async () => {
+    if (!ctxMenu || !syncDir) return
+    const node = ctxMenu.node
+    closeMenu()
+
+    // Avoid clobbering an existing project file with the same name
+    let destName = node.name
+    if (await window.api.pathExists(`${syncDir}/${destName}`)) {
+      const dot = destName.lastIndexOf('.')
+      const stem = dot > 0 ? destName.slice(0, dot) : destName
+      const ext = dot > 0 ? destName.slice(dot) : ''
+      destName = `${stem}-imported${ext}`
+      if (await window.api.pathExists(`${syncDir}/${destName}`)) {
+        useAppStore.getState().setStatusMessage(`Import failed: ${destName} already exists`)
+        return
+      }
+    }
+
+    try {
+      await window.api.copyPath(wsAbs(node), `${syncDir}/${destName}`)
+      useAppStore.getState().setStatusMessage(`Imported ${destName} — syncing to Overleaf`)
+    } catch (e) {
+      useAppStore.getState().setStatusMessage(`Import failed: ${e}`)
+    }
+  }
+
+  const handleWsRename = async () => {
+    if (!ctxMenu || !syncDir) return
+    const node = ctxMenu.node
+    const newName = prompt('New name:', node.name)
+    closeMenu()
+    if (!newName?.trim() || newName === node.name) return
+    const parent = node.path.slice(0, node.path.lastIndexOf('/'))
+    try {
+      await window.api.renamePath(wsAbs(node), `${syncDir}/${parent}/${newName.trim()}`)
+      loadWorkspace()
+    } catch (e) {
+      useAppStore.getState().setStatusMessage(`Rename failed: ${e}`)
+    }
+  }
+
+  const handleWsDelete = async () => {
+    if (!ctxMenu || !syncDir) return
+    const node = ctxMenu.node
+    closeMenu()
+    if (!confirm(`Delete "${node.name}" from workspace?`)) return
+    try {
+      await window.api.deletePath(wsAbs(node))
+      useAppStore.getState().closeTab(node.path)
+      loadWorkspace()
+    } catch (e) {
+      useAppStore.getState().setStatusMessage(`Delete failed: ${e}`)
+    }
+  }
+
+  const handleWsNewFile = async (parentNode?: FileNode) => {
+    if (!syncDir) return
+    closeMenu()
+    const name = prompt('New file name:', 'notes.md')
+    if (!name?.trim()) return
+    const parentPath = parentNode?.isDir ? parentNode.path : 'claude-workspace'
+    try {
+      await window.api.writeFile(`${syncDir}/${parentPath}/${name.trim()}`, '')
+      loadWorkspace()
+    } catch (e) {
+      useAppStore.getState().setStatusMessage(`Create failed: ${e}`)
+    }
+  }
+
+  const handleWsNewFolder = async (parentNode?: FileNode) => {
+    if (!syncDir) return
+    closeMenu()
+    const name = prompt('New folder name:', 'new-folder')
+    if (!name?.trim()) return
+    const parentPath = parentNode?.isDir ? parentNode.path : 'claude-workspace'
+    try {
+      await window.api.mkdirp(`${syncDir}/${parentPath}/${name.trim()}`)
+      loadWorkspace()
+    } catch (e) {
+      useAppStore.getState().setStatusMessage(`Create failed: ${e}`)
+    }
+  }
+
+  const handleRevealInFinder = () => {
+    if (!ctxMenu || !syncDir) return
+    window.api.showInFinder(wsAbs(ctxMenu.node))
+    closeMenu()
+  }
+
+  // ── Drag & drop ──
+
   const [dragOver, setDragOver] = useState(false)
 
   const handleDragOver = useCallback((e: React.DragEvent) => {
@@ -277,13 +454,32 @@ export default function FileTree() {
     e.stopPropagation()
     setDragOver(false)
 
+    const droppedFiles = e.dataTransfer.files
+    if (droppedFiles.length === 0) return
+
+    if (view === 'workspace') {
+      // Copy into the agent workspace on disk (not synced to Overleaf)
+      const dir = useAppStore.getState().syncDir
+      if (!dir) return
+      for (let i = 0; i < droppedFiles.length; i++) {
+        const file = droppedFiles[i]
+        const srcPath = window.api.getPathForFile(file)
+        try {
+          await window.api.copyPath(srcPath, `${dir}/claude-workspace/${file.name}`)
+          useAppStore.getState().setStatusMessage(`Copied ${file.name} to workspace`)
+        } catch (err) {
+          useAppStore.getState().setStatusMessage(`Copy failed: ${err}`)
+          return
+        }
+      }
+      loadWorkspace()
+      return
+    }
+
     const projectId = useAppStore.getState().overleafProjectId
     const folderId = useAppStore.getState().rootFolderId
     if (!projectId || !folderId) return
 
-    const droppedFiles = e.dataTransfer.files
-    if (droppedFiles.length === 0) return
-
     for (let i = 0; i < droppedFiles.length; i++) {
       const file = droppedFiles[i]
       const filePath = window.api.getPathForFile(file)
@@ -298,8 +494,7 @@ export default function FileTree() {
         return
       }
     }
-
-  }, [])
+  }, [view, loadWorkspace])
 
   const handleOpenInOverleaf = () => {
     const projectId = useAppStore.getState().overleafProjectId
@@ -316,19 +511,64 @@ export default function FileTree() {
       onDragLeave={handleDragLeave}
       onDrop={handleDrop}
     >
-      <div className="file-tree-header">
-        <span>FILES</span>
+      <div className="file-tree-header file-tree-tabs">
+        <button
+          className={`file-tree-tab ${view === 'project' ? 'active' : ''}`}
+          onClick={() => setView('project')}
+          title="Overleaf project files (synced)"
+        >
+          Project
+        </button>
+        <button
+          className={`file-tree-tab ${view === 'workspace' ? 'active' : ''}`}
+          onClick={() => setView('workspace')}
+          title="Agent scratch space (claude-workspace/, not synced to Overleaf)"
+        >
+          Workspace
+        </button>
       </div>
+
+      {view === 'workspace' && (
+        <div className="file-tree-ws-toolbar">
+          <button className="file-tree-ws-btn" title="New file" onClick={() => handleWsNewFile()}>＋ File</button>
+          <button className="file-tree-ws-btn" title="New folder" onClick={() => handleWsNewFolder()}>＋ Folder</button>
+          <button className="file-tree-ws-btn" title="Refresh" onClick={loadWorkspace}>↻</button>
+          <button
+            className="file-tree-ws-btn"
+            title="Reveal workspace in Finder"
+            onClick={() => workspaceRoot && window.api.showInFinder(workspaceRoot)}
+          >
+            Finder
+          </button>
+        </div>
+      )}
+
       <div className="file-tree-content">
-        {files.map((node) => (
-          <FileTreeNode key={node.path} node={node} depth={0} onContextMenu={handleContextMenu} />
-        ))}
-        {files.length === 0 && (
-          <div className="file-tree-empty">No files found</div>
+        {view === 'project' ? (
+          <>
+            {files.map((node) => (
+              <FileTreeNode key={node.path} node={node} depth={0} onContextMenu={handleContextMenu} />
+            ))}
+            {files.length === 0 && (
+              <div className="file-tree-empty">No files found</div>
+            )}
+          </>
+        ) : (
+          <>
+            {wsNodes.map((node) => (
+              <WorkspaceNode key={node.path} node={node} depth={0} onContextMenu={handleContextMenu} />
+            ))}
+            {wsNodes.length === 0 && (
+              <div className="file-tree-empty">
+                Workspace is empty — agents use this scratch space for notes,
+                experiments, and generated files. Drop files here to add them.
+              </div>
+            )}
+          </>
         )}
       </div>
 
-      {ctxMenu && (
+      {ctxMenu && ctxMenu.view === 'project' && (
         <div
           ref={menuRef}
           className="context-menu"
@@ -366,6 +606,49 @@ export default function FileTree() {
           </div>
         </div>
       )}
+
+      {ctxMenu && ctxMenu.view === 'workspace' && (
+        <div
+          ref={menuRef}
+          className="context-menu"
+          style={{ left: ctxMenu.x, top: ctxMenu.y }}
+        >
+          {!ctxMenu.node.isDir && (
+            <div className="context-menu-item" onClick={handleImportToProject}>
+              Import to Project
+            </div>
+          )}
+          {ctxMenu.node.isDir && (
+            <div className="context-menu-item" onClick={handleImportToProject}>
+              Import Folder to Project
+            </div>
+          )}
+          <div className="context-menu-item" onClick={handleCopyPath}>
+            Copy Path
+          </div>
+          <div className="context-menu-separator" />
+          <div className="context-menu-item" onClick={handleWsRename}>
+            Rename
+          </div>
+          {ctxMenu.node.isDir && (
+            <>
+              <div className="context-menu-item" onClick={() => handleWsNewFile(ctxMenu.node)}>
+                New File
+              </div>
+              <div className="context-menu-item" onClick={() => handleWsNewFolder(ctxMenu.node)}>
+                New Folder
+              </div>
+            </>
+          )}
+          <div className="context-menu-item" onClick={handleRevealInFinder}>
+            Reveal in Finder
+          </div>
+          <div className="context-menu-separator" />
+          <div className="context-menu-item danger" onClick={handleWsDelete}>
+            Delete
+          </div>
+        </div>
+      )}
     </div>
   )
 }