feat: replace several files with a sqlite db (#3128)

These files have been known to have corruption issues. SQLite will
perform better across filesystems for reads/writes across threads, and
will lock as expected.

I've also put the session file in there, though I'm 50/50 on it - I'll
be replacing it with keyring storage asap anyway.

The key file is _not_ included. It should ~never be changed, and should
be easy for the user to secure + manage themselves

In the future, instead of creating more files, we can just use this as a
kv store

Resolves https://github.com/atuinsh/atuin/issues/2336, resolves
https://github.com/atuinsh/atuin/issues/1650

## Checks
- [ ] I am happy for maintainers to push small adjustments to this PR,
to speed up the review cycle
- [ ] I have checked that there are no existing pull requests for the
same thing

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