That is correct.
One question, is this the directory that you downloaded the source to? If so, that is why there are directories named the same as the executables and they aren't empty. You should put the source code in one directory and use another for the server.
Eg:
/home/main/eqemu/src -> sourcecode goes here
/home/main/eqemu/server -> build the running environment here
You can use any directory names you want. The above is merely examples.
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