Only run the post_clone_commands if the repo is freshly cloned

Dont run them on future runs of soloist.
- Removes hardcoded 'git submodule update --init' call per repo
  - If still using the legacy project syntax we re-add the submodule update since there is no way for that syntax to define a custom command
  - For anyone using the new project syntax if they have submodules that they want initialized then they need to add a post_clone_command to that project entry
- Updates README.md to show new attribute as well as some example uses.

Tracker:[Finishes #74278058] Github:[Closes #5]