Currently, if you want to save a new version of a craft (without loosing the previous one), you need to save it as a completely new craft. This quickly fills the crafts list.
That's why I'm suggesting craft versions. When saving a craft, there could be a second input where you can input a version number. In the crafts list, only the craft would show up (just one instead of all versions). Then, upon clicking that craft, a new window with a list of the saved versions would open so the user can choose a version. To make the version selection easier, you could additionally add a "Load Newest Version" button that loads whatever version was saved last.
Later on, a similar updating system could even be made for the website, but this suggestion is primarily about the game itself.