How can I create a single simulink file from a simulink model, which consists of mutliple linked blocks in user defined block libraries?
In other words I am looking for a way to break all the library links and have the whole model exist in its own file.
You can do this by saving the file using save_system in the Matlab command window, eg. save_system('mysys','mynewfile.mdl','BreakUserLinks','true'). This will break all your library links and save the whole model in one file.
See also help save_system