Particle requires a certain directory structure (not flat, but simple) for inclusion in the web IDE, but a big part of porting a library is generally removing any Arduino-specific code and writing either more general code or Particle specific code.
If you want to hack the makefiles for local building, you can make the directory structure anything you like–that is the beauty of an open-source project.
The author of the JSON library port is around here as @menan I believe, so perhaps he can help.