config: Add a system clock command-line option

This patch adds a 'sys_clock' command-line option and use it to assign
clocks to the system during instantiation.

As part of this change, the default clock in the System class is
removed and whenever a system is instantiated a system clock value
must be set. A default value is provided for the command-line option.

The configs and tests are updated accordingly.

configs/example/ruby_direct_test.py

@@ -93,7 +93,7 @@ else:
 # M5 memory size == Ruby memory size checks
 #
 system = System(physmem = SimpleMemory())
-
+system.clock = options.sys_clock
 #
 # Create the ruby random tester
 #