feat: made --recurse-submodules optional

[jpotw]

History: issue, (closed) pr

Features:

• The --recurse-submodules git command is now only applied when:
  • The user specifies --include-submodules in the CLI.
  • The user selects the "Include submodules" option in the web interface.

Kept changes minimal.
Tests are prepared and ready; I’ll add them once the code is reviewed and confirmed.