I am pretty much a newbie in this regard and haven't found a nice and comprehensive introduction online so far. So I just jumped right in... Xcode set up a lot of things automatically and the rest was trial and error. So I will try to answer your questions as good as a can:
the full error message is:
-bash: ~/Downloads/ExtractPDFMarkUp: Permission denied
It's a plain binary executable (Unix Executable File).
I have compiled it with Xcode based on 64-Bit. The linking is dynamical but I don't know how to change that. I tried all kind of things but wasn't successful. When I rename the dynamic library file on my computer I get a different error message though (something like library not found). I don't know how to get more details. Someone has to do a chmod by hand to get downloaded unix files working.
No, the other people didn't put it on a noexec filesystem.
Thanks!