Thanks for your feedback, it's appreciated.
1. This will be added - currently it's possible in the Viewer and a few other places, but not the builder.
2. In 13.2 there will be a uniform handling of files and folders, but I don't see the point of making py and nc files go into different directories. Perhaps if you are using Windows, make sure to change the ridiculous default setting to hide file extensions in Explorer windows, a.k.a. the best recipe to make users click on virus-infected ".doc.scr" files and fooling users into deleting files by mistake!
3. You can select atoms in the Builder both by clicking them and by drawing a rectangle, and you can move atoms via the Move tool. The second part is trickier, for sure.