feat(git): add git submodules support

[mechanicalbot]

Summary

• Add a GIT_CLONE_SUBMODULES option to clone/update submodules during repository checkout.
• Wire the option through webhook, poll, and init flows so private submodule repos can be fetched.

Motivation

My deployments need secrets stored in a private submodule; cloning with submodules ensures those files are available at deploy time.