SBT throws java.io.FileNotFoundException: (Permission denied) on project folder

The (Permission denied) error says that you're probably running the sbt command from a user that doesn't have permission for the project you're entering sbt in.

Change folder permissions with chown -R youruser:youruser /path/to/project and it should fix it.

The problem could be that you ran sbt as root and few directories inside target folder became root(hence permission denied issue). You can just run sudo rm -rf target/ and then sbt clean compile to regain those compiled files under your account. Worked for me.