Break out custom expect code and enable timeouts when testing.

	* dejagnu/baseboard/atmega128-studio.exp: Break out custom procs
	to separate files, use gdb_stub, not gdb_comm, put GCC and GDB
	specific flags in logical order, don't need status wrapper.
	* dejagnu/gdb-extra.exp: Created.
	* dejagnu/gdb-stub-extra.exp: Created.
	* run-tests.sh: Add --runtestflags, tidy up commenting and help.