I was editing my javascript.js and pressed ctrl s. I assume it works.
But then I noticed in the top, there was an * next to my project name, indicating it did not save.
So this I think, is the problem I mentioned earlier regarding my linked code isn't mirroring properly. I'm hitting CTRL S rather than hitting the save button - so I don't think that linked code is being saved in to other pages!
This actually was the intended behavior. Hitting Ctrl + S while editing a JS file does the same like hitting the "Apply" button - the changes that you do are applied to the design. This causes the design to get marked as changed, so you will need to save it as well.
We decided that this is the best way to do it, as people are used to press "Ctrl/Cmd+S" to save their code when using a regular editor, but I think it would be a mistake to save the entire design when this is done, which his why we only "apply" the changes in the JS editor.
If somebody has a better idea on how this should work we will be happy to hear it and implement it!