Before this fix, the server did not recognize 'short' (as in -a)
options but only 'long' (as in --ansi) options
in the startup command line, due to earlier changes in 5.5
introduced for the performance schema.

The root cause is that handle_options() did not honor the
my_getopt_skip_unknown flag when parsing 'short' options.

The fix changes handle_options(), so that my_getopt_skip_unknown is
honored in all cases.

Note that there are limitations to this,
see the added doxygen documentation in handle_options().

The current usage of handle_options() by the server to
parse early performance schema options fits within the limitations.
This has been enforced by an assert for PARSE_EARLY options, for safety.