Lightning Apps in Salesforce are a great tool to have at your disposal for giving your users a streamlined view of the things they need at their fingertips.
As a quick reminder on how to create a Lightning App go to: Setup –> App Manager –> New Lightning App
Here are all of the things you can control using a Lightning App:
1. Have the App present the user only a subset of tabs (you can choose when building the app if they can modify them or not)
2. Define the type of navigation you want – console or standard. If you choose a console, you would get an extra step during setup for how you want tabs to behave – either as workspace tabs or subtabs of another object.
3. Define if the app is for Phone, Desktop, or both (form factor)
4. Determine if you want a footer bar (Utility bar) and what you want on it
5. Control which profiles or permission sets have access to the App
To update a permission set, go to the permission set –> Assigned Apps –> select or remove the apps you want to be included