Hello Yairm,
Modding is definitely not finalized and as it stands there is no API or consistency with any of that (as of 1.9.2), although, in 2.0 we are looking at addressing these issues by integrating fully into the Steam Workshop. This will allow modders to share/install/uninstall mods in a more permanent fashion by loading brand new files, or overwriting files completely with custom content/features (on/during game load, not after). Of course there will be plenty of compatibility issues to solve there, but at least modders and mod users will have the option.