Modernize repository

I propose we clean up unused implementations in this repository and modernize functionality around filesystem testing and preservation.

Proposed changes:
- [ ] Move `AtomicWriteFile` to `fs` subpackage, its the only root package export that is used today externally (keep in root as deprecated)
- [ ] Remove unused elements from root package, there is no adoption of the manifest format outside of this package
- [ ] Remove unused cmd and FUSE implementations
- [ ] Update `fstest` tests to directly implement the comparisons without the manifest and support `fs.FS`.
- [ ] Deprecate `driver` subpackage in favor of `fs.FS`

For preservation, we should focus more on overlayfs and erofs but no specific proposals for adding functionality as part of this. Also note that composefs offers similar functionality to the manifest defined here but utilizing erofs for metadata. This repository should just provide packages for preserving and comparing filesystems without needing to define its own specification.