Replace "x" for all versions bigger than the version "x" of your current source tree, in_order, and you should be ok. You may want to remove the backup files (some-file-name~ or some-file-name.orig), ...

A project can also start in a folder you pick (Choose a folder… under Start, or --project-folder). If it already has files, you say what they are: the app itself, which the builder edits in place, or ...