Fix: a mod rebuilt with the same name and version but new values (for example Shallow Water Diving 1.0.1) now shows "NOT APPLIED YET" and re-applies, instead of staying on "already installed".
After updating, your installed mods show "NOT APPLIED YET" once - just press Apply.
SHODAN on top of the merger's mods (the recommended order) now shows the mods as installed, "with SHODAN's changes on top", instead of an error. Apply does nothing there.
Adding mods while SHODAN is on top works.
Only changing your mod list with SHODAN on top asks you to Restore in SHODAN, Apply here, then Install in SHODAN again.