Increase project stability by fixing Manifest.toml

[Miles Cranmer]

There are potential problems with only storing Project.toml and not the Manifest.toml file. Simply fixing Project.toml means the Julia dependencies could push patches, and with default PySR settings (update=True), there could be changes to the Julia dependencies which could break small things. For stability reasons, it doesn't seem smart to depend on so many user projects which could push a new patch and potentially break PySR. I think it might be better I manually update the PySR Manifest.toml, do a full run of testing on it, and only then allow any new patches through.