Use `pre-commit-update` to update pre-commit dependencies

[xylar]

Similar to https://github.com/MPAS-Dev/compass/commit/0988504ab0671b38300ba13e7857b37a63cc4991.patch, in .github/workflows/pre_commit_update_workflow.yml we want to switch from pre-commit autoupdate to pre-commit-update to avoid pulling in non-release versions of pre-commit dependencies.