There is no really include paths for the project, since CDT builds mostly not managed. I.e. for makefile project CDT just calls make and include pathsÂ
are managed by make itself. Instead of writing a plugin it may be easier
in this case replace the make command with build.sh command
which will deal with your json and call make, that does not require any plugins
just changing project configuration.
There is such thing as cdt managed project but in this case it won't be driven by make at all, you can look at the code of this in CDT to see how it implements calling of compiler and linker to see if you want to do something similar but I don't recommend it.
For file and project changes google for eclipse resource change listeners.
