A valid way to create an mbed project is to have an .mbed file on the root instead of having the folder under source control.
When hydrating a project of this type (mbed deploy) the following warnings appears which shouldn't be there:
[mbed] WARNING: Program "my-application-1" in "/home/ubuntu/workspace/my-application-1" does not use source control management.
[mbed] WARNING: To fix this you should use "mbed new ." in the root of your program.