diff --git a/apps/desktop/src-tauri/src/latex.rs b/apps/desktop/src-tauri/src/latex.rs
index afb0b53..233d081 100644
--- a/apps/desktop/src-tauri/src/latex.rs
+++ b/apps/desktop/src-tauri/src/latex.rs
@@ -358,6 +358,10 @@ pub async fn compile_latex(
         );
     }
 
+    // Remove stale PDF so a failed compile doesn't return the previous result.
+    let pdf_path = work_dir.join(format!("{}.pdf", main_file_name));
+    let _ = std::fs::remove_file(&pdf_path);
+
     // Run Tectonic in a blocking task (it uses an internal global mutex)
     let work_dir_clone = work_dir.clone();
     let main_file_clone = main_file.clone();
@@ -373,7 +377,6 @@ pub async fn compile_latex(
         compile_result.is_ok()
     );
 
-    let pdf_path = work_dir.join(format!("{}.pdf", main_file_name));
     let log_path = work_dir.join(format!("{}.log", main_file_name));
 
     // Handle "No pages of output" — retry with \AtEndDocument{\null} injection
@@ -893,4 +896,86 @@ Postamble:
         assert!(!dst.path().join("chapters").join("ch1.aux").exists());
         assert!(!dst.path().join(".claudeprism").exists());
     }
+
+    // --- sync_source_files preserves stale PDF (compile_latex deletes it separately) ---
+
+    #[test]
+    fn test_sync_source_files_does_not_copy_pdf_from_source() {
+        // sync_source_files treats .pdf as an artifact and does not copy it.
+        // This means a stale PDF in the build dir survives a sync — the
+        // compile_latex command must delete it explicitly before compiling.
+        let src = tempfile::tempdir().unwrap();
+        let dst = tempfile::tempdir().unwrap();
+
+        std::fs::write(src.path().join("main.tex"), "new content").unwrap();
+        // Simulate a stale PDF already sitting in the build dir
+        std::fs::write(dst.path().join("main.pdf"), "old pdf bytes").unwrap();
+
+        sync_source_files(src.path(), dst.path()).unwrap();
+
+        // Source .tex was synced
+        assert_eq!(
+            std::fs::read_to_string(dst.path().join("main.tex")).unwrap(),
+            "new content"
+        );
+        // Stale PDF in dst was NOT overwritten (sync skips .pdf)
+        // This confirms that compile_latex must delete the PDF itself
+        assert!(dst.path().join("main.pdf").exists());
+        assert_eq!(
+            std::fs::read_to_string(dst.path().join("main.pdf")).unwrap(),
+            "old pdf bytes"
+        );
+    }
+
+    #[test]
+    fn test_sync_source_files_overwrites_changed_tex_content() {
+        // Regression: when a user empties a file, sync must overwrite
+        // the old content in the build dir with the empty content.
+        let src = tempfile::tempdir().unwrap();
+        let dst = tempfile::tempdir().unwrap();
+
+        // Old content in build dir
+        std::fs::write(dst.path().join("main.tex"), "old content").unwrap();
+        // User emptied the file
+        std::fs::write(src.path().join("main.tex"), "").unwrap();
+
+        sync_source_files(src.path(), dst.path()).unwrap();
+
+        assert_eq!(
+            std::fs::read_to_string(dst.path().join("main.tex")).unwrap(),
+            ""
+        );
+    }
+
+    // --- persistent_build_dir ---
+
+    #[test]
+    fn test_stale_pdf_removal_pattern() {
+        // Simulates the pattern used in compile_latex: remove stale PDF
+        // before compilation so a failed compile doesn't return old results.
+        let build_dir = tempfile::tempdir().unwrap();
+        let pdf_path = build_dir.path().join("document.pdf");
+
+        // Simulate previous successful build left a PDF
+        std::fs::write(&pdf_path, "old pdf data").unwrap();
+        assert!(pdf_path.exists());
+
+        // This is what compile_latex does before running tectonic
+        let _ = std::fs::remove_file(&pdf_path);
+        assert!(!pdf_path.exists());
+
+        // If compilation fails, pdf_path.exists() is false → error returned
+    }
+
+    #[test]
+    fn test_stale_pdf_removal_no_existing_file() {
+        // remove_file on a non-existent path should not panic (we use let _ =)
+        let build_dir = tempfile::tempdir().unwrap();
+        let pdf_path = build_dir.path().join("document.pdf");
+
+        assert!(!pdf_path.exists());
+        let result = std::fs::remove_file(&pdf_path);
+        // It's an error but we ignore it with let _ =
+        assert!(result.is_err());
+    }
 }
diff --git a/apps/desktop/src/__tests__/lib/tauri-error-handling.test.ts b/apps/desktop/src/__tests__/lib/tauri-error-handling.test.ts
new file mode 100644
index 0000000..d09bfbf
--- /dev/null
+++ b/apps/desktop/src/__tests__/lib/tauri-error-handling.test.ts
@@ -0,0 +1,56 @@
+import { describe, it, expect } from "vitest";
+
+/**
+ * Regression tests: Tauri IPC error handling.
+ *
+ * When a Rust #[tauri::command] returns Err(String), the frontend's
+ * `invoke()` rejects with a **plain string**, NOT an Error object.
+ * Catch blocks that only check `error instanceof Error` will miss these
+ * and fall through to a generic message, losing the actual error details.
+ *
+ * The correct pattern is:
+ *   error instanceof Error ? error.message
+ *     : typeof error === "string" ? error
+ *     : "Compilation failed"
+ */
+
+/** Helper that mirrors the pattern used in catch blocks */
+function extractErrorMessage(error: unknown): string {
+  return error instanceof Error
+    ? error.message
+    : typeof error === "string"
+      ? error
+      : "Compilation failed";
+}
+
+describe("Tauri IPC error message extraction", () => {
+  it("extracts message from a standard Error object", () => {
+    const error = new Error("Something went wrong");
+    expect(extractErrorMessage(error)).toBe("Something went wrong");
+  });
+
+  it("extracts message from a plain string (Tauri Err(String) pattern)", () => {
+    // This is what Tauri invoke() rejects with for Rust Err(String)
+    const error = "Compilation failed\n\n! Undefined control sequence.";
+    expect(extractErrorMessage(error)).toBe(
+      "Compilation failed\n\n! Undefined control sequence."
+    );
+  });
+
+  it("extracts message from an empty string", () => {
+    expect(extractErrorMessage("")).toBe("");
+  });
+
+  it("falls back to generic message for non-string, non-Error values", () => {
+    expect(extractErrorMessage(42)).toBe("Compilation failed");
+    expect(extractErrorMessage(null)).toBe("Compilation failed");
+    expect(extractErrorMessage(undefined)).toBe("Compilation failed");
+    expect(extractErrorMessage({ code: 1 })).toBe("Compilation failed");
+  });
+
+  it("a plain string is NOT instanceof Error (the root cause of the bug)", () => {
+    const tauriError: unknown = "Compilation failed\n\n! Missing $ inserted.";
+    expect(tauriError instanceof Error).toBe(false);
+    expect(typeof tauriError === "string").toBe(true);
+  });
+});
diff --git a/apps/desktop/src/__tests__/stores/document-store.test.ts b/apps/desktop/src/__tests__/stores/document-store.test.ts
index 90339a7..79ae3dc 100644
--- a/apps/desktop/src/__tests__/stores/document-store.test.ts
+++ b/apps/desktop/src/__tests__/stores/document-store.test.ts
@@ -1,4 +1,5 @@
 import { describe, it, expect, beforeEach, vi } from "vitest";
+import { writeTextFile } from "@tauri-apps/plugin-fs";
 import { useDocumentStore, type ProjectFile } from "@/stores/document-store";
 
 // Mock history store
@@ -252,4 +253,107 @@ describe("useDocumentStore", () => {
       expect(state.selectionRange).toBeNull();
     });
   });
+
+  describe("saveFile", () => {
+    beforeEach(() => {
+      vi.mocked(writeTextFile).mockClear();
+      vi.mocked(writeTextFile).mockResolvedValue(undefined);
+    });
+
+    it("saves a dirty file with content to disk", async () => {
+      useDocumentStore.setState({
+        files: [makeFile({ isDirty: true, content: "saved content" })],
+      });
+      await useDocumentStore.getState().saveFile("main.tex");
+      expect(writeTextFile).toHaveBeenCalledWith("/project/main.tex", "saved content");
+      expect(useDocumentStore.getState().files[0].isDirty).toBe(false);
+    });
+
+    it("saves a dirty file with empty string content (regression: empty content is not falsy-skipped)", async () => {
+      useDocumentStore.setState({
+        files: [makeFile({ isDirty: true, content: "" })],
+      });
+      await useDocumentStore.getState().saveFile("main.tex");
+      expect(writeTextFile).toHaveBeenCalledWith("/project/main.tex", "");
+      expect(useDocumentStore.getState().files[0].isDirty).toBe(false);
+    });
+
+    it("skips saving when content is null", async () => {
+      useDocumentStore.setState({
+        files: [makeFile({ isDirty: true, content: null as unknown as string })],
+      });
+      await useDocumentStore.getState().saveFile("main.tex");
+      expect(writeTextFile).not.toHaveBeenCalled();
+    });
+
+    it("skips saving when file is not dirty", async () => {
+      useDocumentStore.setState({
+        files: [makeFile({ isDirty: false, content: "clean" })],
+      });
+      await useDocumentStore.getState().saveFile("main.tex");
+      expect(writeTextFile).not.toHaveBeenCalled();
+    });
+  });
+
+  describe("saveAllFiles", () => {
+    beforeEach(() => {
+      vi.mocked(writeTextFile).mockClear();
+      vi.mocked(writeTextFile).mockResolvedValue(undefined);
+    });
+
+    it("saves all dirty files", async () => {
+      useDocumentStore.setState({
+        files: [
+          makeFile({ isDirty: true, content: "dirty content" }),
+          makeFile({ id: "clean.tex", name: "clean.tex", absolutePath: "/project/clean.tex", relativePath: "clean.tex", isDirty: false, content: "clean" }),
+        ],
+      });
+      await useDocumentStore.getState().saveAllFiles();
+      expect(writeTextFile).toHaveBeenCalledTimes(1);
+      expect(writeTextFile).toHaveBeenCalledWith("/project/main.tex", "dirty content");
+    });
+
+    it("saves dirty files with empty string content (regression: empty string is not falsy-skipped)", async () => {
+      useDocumentStore.setState({
+        files: [
+          makeFile({ isDirty: true, content: "" }),
+          makeFile({ id: "slide.tex", name: "slide.tex", absolutePath: "/project/slide.tex", relativePath: "slide.tex", isDirty: true, content: "" }),
+        ],
+      });
+      await useDocumentStore.getState().saveAllFiles();
+      expect(writeTextFile).toHaveBeenCalledTimes(2);
+      expect(writeTextFile).toHaveBeenCalledWith("/project/main.tex", "");
+      expect(writeTextFile).toHaveBeenCalledWith("/project/slide.tex", "");
+      // Both should be marked clean
+      const files = useDocumentStore.getState().files;
+      expect(files.every((f) => !f.isDirty)).toBe(true);
+    });
+
+    it("skips files with null content even if dirty", async () => {
+      useDocumentStore.setState({
+        files: [
+          makeFile({ isDirty: true, content: null as unknown as string }),
+        ],
+      });
+      await useDocumentStore.getState().saveAllFiles();
+      expect(writeTextFile).not.toHaveBeenCalled();
+    });
+  });
+
+  describe("setPdfData / setCompileError", () => {
+    it("setPdfData clears compile error", () => {
+      useDocumentStore.setState({ compileError: "some error" });
+      useDocumentStore.getState().setPdfData(new Uint8Array([1, 2, 3]));
+      const state = useDocumentStore.getState();
+      expect(state.pdfData).toEqual(new Uint8Array([1, 2, 3]));
+      expect(state.compileError).toBeNull();
+    });
+
+    it("setCompileError stores the error string (regression: Tauri string errors must be preserved)", () => {
+      useDocumentStore.getState().setCompileError("Compilation failed\n\n! Undefined control sequence.");
+      expect(useDocumentStore.getState().compileError).toBe(
+        "Compilation failed\n\n! Undefined control sequence."
+      );
+    });
+  });
 });
diff --git a/apps/desktop/src/components/claude-chat/chat-composer.tsx b/apps/desktop/src/components/claude-chat/chat-composer.tsx
index 667e0ac..56022d6 100644
--- a/apps/desktop/src/components/claude-chat/chat-composer.tsx
+++ b/apps/desktop/src/components/claude-chat/chat-composer.tsx
@@ -30,7 +30,7 @@ function getFileIcon(file: ProjectFile) {
   return <FileTextIcon className="size-3.5 shrink-0 text-muted-foreground" />;
 }
 
-export const ChatComposer: FC = () => {
+export const ChatComposer: FC<{ isOpen?: boolean }> = ({ isOpen }) => {
   const sendPrompt = useClaudeChatStore((s) => s.sendPrompt);
   const cancelExecution = useClaudeChatStore((s) => s.cancelExecution);
   const isStreaming = useClaudeChatStore((s) => s.isStreaming);
@@ -86,6 +86,15 @@ export const ChatComposer: FC = () => {
   const pendingAttachments = useClaudeChatStore((s) => s.pendingAttachments);
   const consumePendingAttachments = useClaudeChatStore((s) => s.consumePendingAttachments);
 
+  // Focus textarea when the drawer opens
+  const prevOpenRef = useRef(false);
+  useEffect(() => {
+    if (isOpen && !prevOpenRef.current) {
+      setTimeout(() => textareaRef.current?.focus(), 0);
+    }
+    prevOpenRef.current = !!isOpen;
+  }, [isOpen]);
+
   useEffect(() => {
     if (pendingAttachments.length === 0) return;
     const attachments = consumePendingAttachments();
@@ -697,7 +706,6 @@ export const ChatComposer: FC = () => {
             onPaste={handlePaste}
             placeholder="Ask me anything (/ for commands, @ to mention)"
             className="max-h-40 min-h-10 w-full resize-none bg-transparent px-4 py-2 text-sm outline-none placeholder:text-muted-foreground"
-            autoFocus
             rows={1}
           />
         )}
diff --git a/apps/desktop/src/components/claude-chat/claude-chat-drawer.tsx b/apps/desktop/src/components/claude-chat/claude-chat-drawer.tsx
index a108363..9e82748 100644
--- a/apps/desktop/src/components/claude-chat/claude-chat-drawer.tsx
+++ b/apps/desktop/src/components/claude-chat/claude-chat-drawer.tsx
@@ -145,7 +145,7 @@ export function ClaudeChatDrawer() {
         </div>
 
         {/* Composer */}
-        <ChatComposer />
+        <ChatComposer isOpen={isOpen} />
       </div>
     </div>
   );
diff --git a/apps/desktop/src/components/workspace/editor/latex-editor.tsx b/apps/desktop/src/components/workspace/editor/latex-editor.tsx
index 0203841..9d78df1 100644
--- a/apps/desktop/src/components/workspace/editor/latex-editor.tsx
+++ b/apps/desktop/src/components/workspace/editor/latex-editor.tsx
@@ -278,7 +278,7 @@ export function LatexEditor() {
       const data = await compileLatex(projectRoot, targetFile);
       setPdfData(data);
     } catch (error) {
-      setCompileError(error instanceof Error ? error.message : "Compilation failed");
+      setCompileError(error instanceof Error ? error.message : typeof error === "string" ? error : "Compilation failed");
     } finally {
       setIsCompiling(false);
     }
@@ -782,7 +782,7 @@ export function LatexEditor() {
         )}
         <ClaudeChatDrawer />
         {/* Selection toolbar */}
-        {toolbarPosition && selectionLabel && !isMergeActiveRef.current && (
+        {toolbarPosition && selectionLabel && !isMergeActiveRef.current && !isSearchOpen && (
           <SelectionToolbar
             position={toolbarPosition}
             contextLabel={selectionLabel}
diff --git a/apps/desktop/src/components/workspace/preview/pdf-preview.tsx b/apps/desktop/src/components/workspace/preview/pdf-preview.tsx
index af7a8ce..dd83fbc 100644
--- a/apps/desktop/src/components/workspace/preview/pdf-preview.tsx
+++ b/apps/desktop/src/components/workspace/preview/pdf-preview.tsx
@@ -60,10 +60,10 @@ export function PdfPreview() {
   const files = useDocumentStore((s) => s.files);
   const saveAllFiles = useDocumentStore((s) => s.saveAllFiles);
   const setActiveFile = useDocumentStore((s) => s.setActiveFile);
-  const activeFileType = useDocumentStore((s) => {
-    const active = s.files.find((f) => f.id === s.activeFileId);
-    return active?.type ?? "tex";
+  const activeFile = useDocumentStore((s) => {
+    return s.files.find((f) => f.id === s.activeFileId) ?? null;
   });
+  const activeFileType = activeFile?.type ?? "tex";
   const isTexActive = activeFileType === "tex";
   const requestJumpToPosition = useDocumentStore(
     (s) => s.requestJumpToPosition,
@@ -277,20 +277,21 @@ export function PdfPreview() {
       setIsCompiling(true);
       try {
         await saveAllFiles();
-        const mainFile = files.find((f) => f.name === "document.tex" || f.name === "main.tex");
-        const mainFileName = mainFile?.relativePath || "document.tex";
-        const data = await compileLatex(projectRoot, mainFileName);
+        const targetFile = activeFile?.type === "tex"
+          ? activeFile.relativePath
+          : (files.find((f) => f.name === "document.tex" || f.name === "main.tex")?.relativePath || "document.tex");
+        const data = await compileLatex(projectRoot, targetFile);
         setPdfData(data);
       } catch (error) {
         setCompileError(
-          error instanceof Error ? error.message : "Compilation failed",
+          error instanceof Error ? error.message : typeof error === "string" ? error : "Compilation failed",
         );
       } finally {
         setIsCompiling(false);
       }
     };
     compile();
-  }, [initialized, projectRoot, pdfData, isCompiling, compileError, setIsCompiling, setPdfData, setCompileError, saveAllFiles, files]);
+  }, [initialized, projectRoot, pdfData, isCompiling, compileError, setIsCompiling, setPdfData, setCompileError, saveAllFiles, files, activeFile]);
 
   const zoomIn = () => setScale((s) => Math.min(4, s + 0.1));
   const zoomOut = () => setScale((s) => Math.max(0.25, s - 0.1));
@@ -320,12 +321,13 @@ export function PdfPreview() {
     setPdfError(null);
     try {
       await saveAllFiles();
-      const mainFile = files.find((f) => f.name === "document.tex" || f.name === "main.tex");
-      const mainFileName = mainFile?.relativePath || "document.tex";
-      const data = await compileLatex(projectRoot, mainFileName);
+      const targetFile = activeFile?.type === "tex"
+        ? activeFile.relativePath
+        : (files.find((f) => f.name === "document.tex" || f.name === "main.tex")?.relativePath || "document.tex");
+      const data = await compileLatex(projectRoot, targetFile);
       setPdfData(data);
     } catch (error) {
-      setCompileError(error instanceof Error ? error.message : "Compilation failed");
+      setCompileError(error instanceof Error ? error.message : typeof error === "string" ? error : "Compilation failed");
     } finally {
       setIsCompiling(false);
     }
diff --git a/apps/desktop/src/hooks/use-claude-events.ts b/apps/desktop/src/hooks/use-claude-events.ts
index 8fda935..e600003 100644
--- a/apps/desktop/src/hooks/use-claude-events.ts
+++ b/apps/desktop/src/hooks/use-claude-events.ts
@@ -244,22 +244,28 @@ export function useClaudeEvents() {
       const docStore = useDocumentStore.getState();
       await docStore.refreshFiles();
 
-      // Auto-recompile after Claude finishes — always attempt if a tex file exists.
+      // Auto-recompile after Claude finishes.
+      // Prefer the active file if it's a .tex file; fall back to document.tex / main.tex.
       // Skip if another compilation is already in progress (e.g. initial compile).
-      const { projectRoot, files, isCompiling: alreadyCompiling } = useDocumentStore.getState();
+      const { projectRoot, files, activeFileId, isCompiling: alreadyCompiling } = useDocumentStore.getState();
       if (projectRoot && !alreadyCompiling) {
-        const mainFile = files.find(
-          (f) => f.name === "document.tex" || f.name === "main.tex",
-        );
-        if (mainFile) {
-          const mainFileName = mainFile.relativePath;
+        const activeFile = files.find((f) => f.id === activeFileId);
+        const targetFile =
+          activeFile?.type === "tex"
+            ? activeFile
+            : files.find((f) => f.name === "document.tex" || f.name === "main.tex");
+        if (targetFile) {
+          const mainFileName = targetFile.relativePath;
           useDocumentStore.getState().setIsCompiling(true);
           try {
+            // Flush any dirty files to disk before compiling so the
+            // compiler (which reads from disk) sees the latest content.
+            await useDocumentStore.getState().saveAllFiles();
             const pdfData = await compileLatex(projectRoot, mainFileName);
             useDocumentStore.getState().setPdfData(pdfData);
           } catch (err) {
             useDocumentStore.getState().setCompileError(
-              err instanceof Error ? err.message : "Compilation failed",
+              err instanceof Error ? err.message : typeof err === "string" ? err : "Compilation failed",
             );
           } finally {
             useDocumentStore.getState().setIsCompiling(false);
diff --git a/apps/desktop/src/stores/document-store.ts b/apps/desktop/src/stores/document-store.ts
index 8194e4d..625e907 100644
--- a/apps/desktop/src/stores/document-store.ts
+++ b/apps/desktop/src/stores/document-store.ts
@@ -95,7 +95,7 @@ function scheduleAutoSave() {
     const store = storeRef;
     if (!store) return;
     const state = store.getState();
-    const dirtyFiles = state.files.filter((f) => f.isDirty && f.content);
+    const dirtyFiles = state.files.filter((f) => f.isDirty && f.content != null);
     if (dirtyFiles.length > 0) {
       await state.saveAllFiles();
     }
@@ -347,7 +347,7 @@ export const useDocumentStore = create<DocumentState>()((set, get) => ({
   saveFile: async (id) => {
     const state = get();
     const file = state.files.find((f) => f.id === id);
-    if (!file || !file.isDirty || !file.content) return;
+    if (!file || !file.isDirty || file.content == null) return;
 
     await writeTexFileContent(file.absolutePath, file.content);
     set((s) => ({
@@ -359,7 +359,7 @@ export const useDocumentStore = create<DocumentState>()((set, get) => ({
 
   saveAllFiles: async () => {
     const state = get();
-    const dirtyFiles = state.files.filter((f) => f.isDirty && f.content);
+    const dirtyFiles = state.files.filter((f) => f.isDirty && f.content != null);
     const results = await Promise.allSettled(
       dirtyFiles.map((f) => writeTexFileContent(f.absolutePath, f.content!)),
     );