Preserve local paths for desktop saves (#5543)

# Summary

- Adds desktop file tracking: local paths are preserved and save buttons
now work as expcted (doing Save/Save As as appropriate)
- Adds logic to track whether files are 'dirty' (they've been modified
by some tool, and not saved to disk yet).
- Improves file state UX (dirty vs saved) and close warnings
- Web behaviour should be unaffected by these changes

## Indicators
Files now have indicators in desktop mode to tell you their state.

### File up-to-date with disk

<img width="318" height="393" alt="image"
src="https://github.com/user-attachments/assets/06325f9a-afd7-4c2f-8a5b-6d11e3093115"
/>

### File modified by a tool but not saved to disk yet

<img width="357" height="385" alt="image"
src="https://github.com/user-attachments/assets/1a7716d9-c6f7-4d13-be0d-c1de6493954b"
/>

### File not tracked on disk

<img width="312" height="379" alt="image"
src="https://github.com/user-attachments/assets/9cffe300-bd9a-4e19-97c7-9b98bebefacc"
/>

# Limitations
- It's a bit weird that we still have files stored in indexeddb in the
app, which are still loadable. We might want to change this behaviour in
the future
- Viewer's Save doesn't persist to disk. I've left that out here because
it'd need a lot of testing to make sure the logic's right with making
sure you can leave the Viewer with applying the changes to the PDF
_without_ saving to disk
- There's no current way to do Save As on a file that has already been
persisted to disk - it's only ever Save. Similarly, there's no way to
duplicate a file.

---------

Co-authored-by: James Brunton <[email protected]>
Co-authored-by: James Brunton <[email protected]>

frontend/src/desktop/hooks/useOpenedFile.ts

@@ -1,10 +1,23 @@
-import { useState, useEffect } from 'react';
+import { useState, useEffect, useRef, useCallback } from 'react';
 import { fileOpenService } from '@app/services/fileOpenService';
 import { listen } from '@tauri-apps/api/event';
 
 export function useOpenedFile() {
   const [openedFilePaths, setOpenedFilePaths] = useState<string[]>([]);
   const [loading, setLoading] = useState(true);
+  const openedFilePathsRef = useRef<string[]>([]);
+
+  const clearOpenedFilePaths = useCallback(() => {
+    openedFilePathsRef.current = [];
+    setOpenedFilePaths([]);
+  }, []);
+
+  const consumeOpenedFilePaths = useCallback(() => {
+    const current = openedFilePathsRef.current;
+    openedFilePathsRef.current = [];
+    setOpenedFilePaths([]);
+    return current;
+  }, []);
 
   useEffect(() => {
     // Function to read and process files from storage
@@ -16,8 +29,8 @@ export function useOpenedFile() {
 
         if (filePaths.length > 0) {
           console.log(`✅ Found ${filePaths.length} file(s) in storage:`, filePaths);
+          openedFilePathsRef.current = filePaths;
           setOpenedFilePaths(filePaths);
-          await fileOpenService.clearOpenedFiles();
         }
       } catch (error) {
         console.error('❌ Failed to read files from storage:', error);
@@ -44,5 +57,5 @@ export function useOpenedFile() {
     };
   }, []);
 
-  return { openedFilePaths, loading };
+  return { openedFilePaths, loading, clearOpenedFilePaths, consumeOpenedFilePaths };
 }