Без скрытых папок и файлов в каталоге:
zip -r zipfile.zip directory/*
каталог: |── .git │ ├── src │ └── Work.file ├── .test │ └── .file └── test.file
$ zip -r zipfile.zip directory/*
adding: directory/src/ (stored 0%)
adding: directory/src/Work.file (stored 0%)
adding: directory/test.file (stored 0%)