Fix option parsing infrastructure bug.

Fix option parsing infrastructure bug.

In main.c: used adjusted string with placeholers for removed options (so flag
values don't move based on config, allowing FORCE_FLAGS to work).

In scripts/mkflags.c: test was wrong, a bare longopt never matches a single
letter command, but it was treated as always matching when comparing
allyesconfig vs current config to determine which options were disabled, so
there was a corner case that got the flag values wrong.