Maybe a combination of private fork with comments and separate markdown files with notes (maybe in the same private fork) Consider using special "symbols" in c

Maybe a combination of private fork with comments and separate markdown files with notes (maybe in the same private fork) Consider using special "symbols" in comments like "MYDOCS_XXX" that you search for in your modified version of the code base, and refer to in other places. These will survive renames of function names etc by the upstream authors.