Okay, let’s try this: remove everything Particle-dev, ParticleJS, Particle-whatever related. I think a bunch of things have been confused. The Particle Dev is an editor based on the Atom editor by GitHub, and is a standalone program. ParticleJS is the Javascript SDK meant to be used when you’re trying to create a node.js or browser application and want an easy API wrapper. The Dev and SDK have nothing to do with each other, and operate completely independently.
Try to get rid of any Particle Dev files as thoroughly as possible, so they won’t mess up a new installation. Then, download the Dev again, and go through the installation process.
Then, create a nice, clean, empty new directory. In that directory, paste nothing more than the WebServer.h file and your WhatEverYouLikeToCallIt.ino file. Don’t make any subdirectories, don’t add any other files.
I’ve just done a fresh install of Particle Dev, and the steps above allowed me to successfully compile for the Core without the issues you’ve mentioned above.
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