1. Site owner has placed custom modules in `modules/contrib` 2. Site owner has placed contributed modules in both `modules` and `modules/contrib`. 3. Provide a custom `template.gitignore`. Add option `--gitignore=my.gitignore`. 4. Do not touch .gitignore. Add `--no-gitignore` option.
modules/contribmodulesandmodules/contrib.template.gitignore. Add option--gitignore=my.gitignore.--no-gitignoreoption.