[Chore] Update `cargo.toml` repository links

[raychu86]

Motivation

This PR is mainly cleanup and updating inaccurate links.

This PR updates the old references to AleoHQ/snarkOS with the new AleoNet/snarkOS. This also fixes the lockfile issue of having mixed snarkVM versions and bumps the self_update crate version.

Related to https://github.com/AleoNet/snarkVM/pull/2512.

Also resolves - https://github.com/AleoNet/snarkOS/pull/3334

Full CI ran here