In that case, how about this suggestion: Use the file command (in a loop, probably driven by a find command) to determine the file types of all files in your source tree. Then use sort/uniq to count how many there are of each type. For example, you might find "1234: C++ source", "45: Makefile", and "3: ELF 64-bit executable". If you get really unlucky, there will be an entry for "data", meaning file was not able to classify the file. Then go over each file type that you recognize as binary (there should be very few if this is a traditional source tree), and see what's up.
Obnoxious remark: Today, there is nothing wrong with putting binary files under source control. Modern SCM systems handle that just fine.