Add option to temporarily remove files before checkout and copy them back once branch is checked out

[matfire]

As of v0.6.0, any file that is not part of the tree (like a .env file) is lost after a checkout. The temporary solution is just to have it stored elsewhere and add a command to the list that copies it over (since the commands are executed after the checkout, the file is available when the app starts back up).

I should probably have a nicer solution: a list of files to be configured with the application:

[apps.test]
# all the other options
preservedFiles=['.env']

This would allow the program to store them in a temporary folder, checkout the newly released tag and copy them back over once all was done.