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Distribution: Various, Ubuntu, Fedora, Open Solaris, Solaris, RHEL, CentOS
Makefiles can be a bit of black magic even to those of us who have written our own!
If the program and makefile have been well written you can probably move the binary to your desired location after compilation with no adverse effects, but I make no guarantee. I've certianly been able to do this with a huge project I worken on (and I never had a configure option in my makefile!).
You make also find that /usr/local/bin is a better place for the binary, it is usually already in your path, therefore if you need to run that binary or call it from a script you don't need to mess around adding to your path.
Alternatively, make it somewhere like /opt and make a link to the binary in /home/Master_9/bin (or /usr/local/bin).
Sorry I haven't been able to help more. If you need help making the links, just let us know.