Ad hoc analysis
Alice is an data analyst / computational scientist starting a new project. She creates a folder in her linux home directory and populates it with a set of files (e.g. starting data). She starts some exploratory statistical analysis in an interactive R session. After some time she arrives at some preliminary findings she wants to share with a biologist (Bob) she is collaborating with. At this point she 1. creates a new Synapse project and 2. invites Bob to join the project (probably through Synapse web client). At OS command line, she runs a command like:
syn add . syn1234 -recurse = true -location = local //Where syn1234 is syn id of her project.
or, more naturally
syn add . AlicesProject - recurse = true -location = local
At this point the Synapse project is populated with a mirror of her local filesystem, although all the files are still living exclusively on her local file system.