Enable template users to more easily contribute back to configuration

[dustinlyons]

1. Create two new repositories for each template, starter and starter-with-secrets
2. Change initialize scripts to leverage new repository so users can easily open PRs back to their configuration if they want to
3. Link repositories back to this configuration via git submodules
4. Change existing scripts to abstract away any submodule commands

Notes:

• For CI, use Claude or something similar to help apply patches across repositories for now
• We probably want to refactor secrets into a dependency that is enabled/disable, not two repositories
• We can continue to use sed to replace files, mainly replacing instances of starter with starter-with-secrets, potentially supporting a blacklist of files not to automatically edit