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/core/tools/EditTableOfContents.tsx

@@ -1,5 +1,6 @@
 import { useCallback, useEffect, useMemo, useRef, useState } from 'react';
 import { useTranslation } from 'react-i18next';
+import { downloadFile } from '@app/services/downloadService';
 import MenuBookRoundedIcon from '@mui/icons-material/MenuBookRounded';
 import { alert } from '@app/components/toast';
 import { createToolFlow } from '@app/components/tools/shared/createToolFlow';
@@ -191,14 +192,7 @@ const EditTableOfContents = (props: BaseToolProps) => {
   const exportJsonCallback = () => {
     const data = JSON.stringify(serializeBookmarkNodes(base.params.parameters.bookmarks), null, 2);
     const blob = new Blob([data], { type: 'application/json' });
-    const url = URL.createObjectURL(blob);
-    const anchor = document.createElement('a');
-    anchor.href = url;
-    anchor.download = 'bookmarks.json';
-    document.body.appendChild(anchor);
-    anchor.click();
-    document.body.removeChild(anchor);
-    URL.revokeObjectURL(url);
+    void downloadFile({ data: blob, filename: 'bookmarks.json' });
     alert({
       title: t('editTableOfContents.messages.exported', 'JSON download ready'),
       alertType: 'success',