> For some years I was thinking about using CLIPS for algorithmic music composition

This is a great use case! I'd be interested in seeing what you come up with.

> in which format the code/rule-base is kept

When you use constructs-to-c, the generated C files represent your rules engine constructs as pointers to pointers of CLIPSLexeme, CLIPSFloat, CLIPSInteger, and CLIPSBitMap structs. It does not store it as the raw clips code fed into the interpreter. You can later use functions like `save-facts` to generate the rules in CLIPS syntax based on these pointers to pointers of structs.