Fix deprecations

[cticenhour]

This PR:

• Updates the MOOSE submodule.
• Updates the .gitignore file in order to ignore new YAML files for metadata generated during make as well as a dotfolder produced by VSCode.
• Transitions from the ModulesApp::registerAll(...) method in CraneApp.C to ModulesApp::registerAllObjects<CraneApp>(...), which is now preferred for dynamic linking. This one is affecting Zapdos as well.
• Runs HIT format to remove legacy syntax in CRANE input files.
• Transitions from the deprecated [TimeStepper] block syntax to that of [TimeSteppers]

Tagging @smpeyres for a review.

[cticenhour]

Feel free to merge whenever - Zapdos CI checks for CRANE updates weekly on Friday evening.

[smpeyres]

@cticenhour Tried to merge earlier - something about signing commits is blocking the merge. Never had to do this before -- I'll try to figure it out tomorrow afternoon!

[smpeyres]

@cticenhour The merge is blocked because "the base branch requires all commits to be signed". From what I can tell from https://docs.github.com/en/authentication/managing-commit-signature-verification/signing-commits, it seems you would have to sign each of the commits...

Since you have already committed them, maybe there is a work around? @dcurreli This signed commit thing seems new...

[cticenhour]

This setting is part of the repository branch protection rules and has to be turned on manually. Did those settings change recently?

[smpeyres]

It seems so... Wasn't my doing!

[cticenhour]

@smpeyres Alright....since I don't want to wait on this anymore, I have signed these commits on my local machine, so this is ready to be merged.

[smpeyres]

@smpeyres Alright....since I don't want to wait on this anymore, I have signed these commits on my local machine, so this is ready to be merged.

Can't blame you, but I'm able to merge now. Thank you!