I'll try to answer it, but you'll have to clarify some questions....
1. What do you mean by "the extension of x++"? Code is store in the modelstore DB and executed on server (X++ and CIL) and client (X++).
2. What's your definiton of "source file of compilation" and which language are you talking about in this question?
3. Compiled code is stored in the modelstore database. That's why you don't have to recompile the application when you deploy the whole modelstore.
4. The the content of /source/ is used fopr debugging - it's the code you see in debugger when you debug CIL.
5. You probably meant how it generates CIL, not p-code. What exactly do you want to know about it?
6. CIL compiler reads compiled X++ code (p-code) stored in the modelstore database, generates a CIL assembly and puts it back. No .axmodelstore file is used during compilation.