Placing module code in local modules folder doesn't appear to be located by Native IDE

What changed on the WebIDE and server side?

Nothing at all to do with projects has changed. This is 100% something that has changed on your PC. As far as I'm aware you are basically the only user that's hitting this out of thousands of Web IDE users.

While someone could possibly rewrite the way 'projects' handles loading files the whole situation is a bit of a mess with Projects only working on Chrome apps (and windows native), which is deprecated and disappearing soon anyway. At some point I'd like to add an online element to the IDE that'd just pull files from a user account espruino.com and avoid all this, but that is some way off.

Honestly all I can suggest is to put your modules online or on a local webserver and instead require them via URL.

Or is defragmentation still a thing on your PC? If so, I'd do that - it might be that just having a less fragmented hard disk would speed up the access time and would fix your problems.

Failing that - time to upgrade to an SSD?