docs(applications): explain private git submodules

[vaguul]

Changes

• Expand the Applications Git Submodules section with private submodule guidance.
• Document GitHub App/deploy key access requirements for parent and submodule repositories.
• Add the relative .gitmodules URL pattern that resolves the common private GitHub authentication failure.
• Clarify that submodule-only commits do not update the parent repository's submodule pointer by themselves.

Issue

• Closes Document how to use private Git submodules with Coolify #343

Testing

• git diff --check
• Not run: local docs build/typecheck, because this checkout has no bun command or node_modules installed.