Implement a Flatpak and fix dependencies
- Implement Flatpak compatibility
- Force the Protobuf Python module to 6.x as 7.x removes the FieldDescriptor.label field and other stuff (https://protobuf.dev/news/2025-09-19/#python-remove-apis)
- Bump the target Python version specified in pyproject.toml to 3.9+ to content Dependabot