Ensure that media files have the correct permissions (read-write)

[aplaice]

I believe that the issue which I encountered is that, with flatpak-installed Anki, if one CrowdAnki-imports a deck with media, then (depending on the location of the file source), these files might be read-only (from the PoV of flatpak), so when copying them into Anki's collection.media/, they're kept as read-only.

This leads to an issue when re-importing, since then Anki/CrowdAnki can't overwrite the files.

To reproduce

(On Linux)

1. Using flatpak-installed Anki (25.09.2) import a deck (containing media) using CrowdAnki: import from disk, from a folder within ~/Downloads/.
2. (Optionally) Check the file permissions of the newly imported media (the media should be at ~/.var/app/net.ankiweb.Anki/data/Anki2/User 1/collection.media/)
3. Re-import the same deck using CrowdAnki.

Expected behaviour

1. The deck is imported.
2. The media are rw.
3. The deck is re-imported.

Actual behaviour

1. The deck is imported.
2. The media are read-only (r).
3. Re-import causes a crash:

Details

Anki 25.09.2 (3890e12c) (ao)
Python 3.12.11 Qt 6.9.3 PyQt 6.9.1
Platform: Linux-6.8.0-84-generic-x86_64-with-glibc2.40

Traceback (most recent call last):
  File "/home/adam/.var/app/net.ankiweb.Anki/data/Anki2/addons21/1788670778/anki/ui/action_vendor.py", line 32, in <lambda>
    lambda: AnkiJsonImporter.import_deck(self.window.col, self.directory_vendor))
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/adam/.var/app/net.ankiweb.Anki/data/Anki2/addons21/1788670778/importer/anki_importer.py", line 112, in import_deck
    AnkiJsonImporter.import_deck_from_path(collection, Path(directory_path))
  File "/home/adam/.var/app/net.ankiweb.Anki/data/Anki2/addons21/1788670778/importer/anki_importer.py", line 101, in import_deck_from_path
    if importer.load_deck(directory_path):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/adam/.var/app/net.ankiweb.Anki/data/Anki2/addons21/1788670778/importer/anki_importer.py", line 42, in load_deck
    self.import_media(directory_path)
  File "/home/adam/.var/app/net.ankiweb.Anki/data/Anki2/addons21/1788670778/importer/anki_importer.py", line 56, in import_media
    shutil.copy(full_filename, self.collection.media.dir())
  File "/usr/lib/python3.12/shutil.py", line 435, in copy
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/usr/lib/python3.12/shutil.py", line 262, in copyfile
    with open(dst, 'wb') as fdst:
         ^^^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied: '/home/adam/.var/app/net.ankiweb.Anki/data/Anki2/User 1/collection.media/ug-flag-tajikistan.svg'

===Add-ons (active)===
(add-on provided name [Add-on folder, installed at, version, is config changed])
CrowdAnki JSON exportimport Edit history Collaborate on deck creation ['1788670778', 2023-10-30T19:57, 'None', '']

===IDs of active AnkiWeb add-ons===
1788670778

===Add-ons (inactive)===
(add-on provided name [Add-on folder, installed at, version, is config changed])

(NB the same error occurs for CrowdAnki from AnkiWeb and from git.)

Further info

I have not tested with latest Anki not from flatpak because I can't easily get it to run (according to Anki, Ubuntu LTS 22.04 is apparently not "a modern Linux distro" :/), so my belief that this is linked to flatpak is only a strong suspicion.

Some solutions:

1. run os.chmod afterwards
2. Just use shutil.copyfile, since shutil.copy is basically copyfile(...) + copymode(...) and we simply don't want the second part. (What are the "default" permissions?) (OTOH I'm not sure how this would mesh with non-Linux platforms (default permissions there).)

---

Later aside: export with flatpak also doesn't work, at all, due to create directory permission errors.