Godot: Jetbrains is overwriting my dependency changes I am trying to fix from the Godot editor

I have no idea why this is happening but I changed my script files locations, fixed the dependencies and if I load up godot by itself, it's fine.  But if I open a gd file in jetbrains, and use the player debug, it reverts all my old changes to god knows what. Then godot alerts me that the files were changed externally.  I am going to ask for a refund if there isn't an easy solution to this madness.