Dan:
I'm going to have to examine the byte code to determine the package (in the constant pool).
(Although I dont know what do you intend when you say "in the constant pool" but I will try to answer.)
You mean that you will scan all the entries in the jar file and assert the package of the class by removing src from the path?
OR
You want to parse every entry in the jar and then determine the package by reading the compiled byte code?
If you can not change the jar file, I think you will be better off exploding the jar file onto the file system and add src/ to the classpath rather than doing all the jugglery.
I strongly feel that the structure of the jar must be changed to include the path from com and not from src.