I got the api files working correctly now.
These are the files now:
Oxygen.api - this will be only touched by Charles, for user defined types, classes, methods and keywords Charles writes for Oxygen
OpenGL.api - pulled the opengl stuff into its own api file, only touched by Charles if need be
Win.api - pulled it out also to its own api file, only touched by Charles if need be
User.api - this will be where users add their own user defined types, classes and class methods tips
I updated Oxygen.properties to use the above api files correctly and also updated the reference.
That attachment has been removed as it is now in the Oxygen download updated by Charles.