In the past Visual Studio simply updated solution based on files added in Unity but now all of them have to be added manually and they are as miscellaneous when they are added. How can I fix it?
I have run into this a few times. It is some particular workflow that causes it to happen. I usually create new files from within visual studio instead of unity and it seems to avoid the issue. If you do have files currently marked as miscellaneous, you can right click them in visual studio and exclude them from the project and then re-add them to fix the issue. You will need to show all files to re-add the file (show all files button is at the top of the solution explorer).
Hope this helps :)