Improve portability of getopt reset #1545
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getopt reset is done sometimes with "optind = 0", sometimes with "optind = 1". Unfortunately, neither is portable. For example, if the bundled getopt see "optind = 1" on the very first call it will implicitly add a dash in front of the first argument; and while some glibc versions even had reports of crashes if reset with "optind = 1", Apple's getopt did the same for "optind = 0".
Since we know that there will always be two getopt calls only, of which the first will be in ReadFlags, place the ugly code there so that it is not replicated all over ninja.cc.