Did you run configure after running the installer? If you didn't the Makefiles won't get updated properly and these errors occur.
If you did run configure, did you by any chance install the patch manually? In this case you probably forgot to run the installer after applying the source patch, therefore your Makefiles don't include the Harmony source files. You can also use the script in Server/Manual Install/harmony_addfiles.sh to automatically patch the makefiles. Don't forget to run configure here as well.
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