I'm not sure if "gcc" is supposed to handle both c++ and plain c programs, but the arduino IDE is careful to use "gcc" or "g++" explicitly. Also notice that it has very explicit command-line paths specified for Include files and libraries. To build from a normal command line, you would have to duplicate those path specifications, or move the files to a more standard location, or copy them locally, or have them in the makefiles, or some combination of those...