Restructure

This MR is non-functional (i.e. should have no impact on functionality):

• it modifies the file tree; packages for git and cli have been created, and the package specification has been removed
• it adds and modifies type hints to be more precise
• it adds minimal docstrings for the fs modules
• it changes the order of methods (plus properties, etc.) for most classes
• it renames a few classes and functions