src/configure: remove --enable-run-in-place

It's been deprecated since at least 2.4.0, time to remove it.  Configure
without providing a --prefix instead.
src/configure: use AS_HELP_STRING() everywhere

This makes the line-wrapping of the --help output automatic.

There are also some minor cosmetic changes to the help text: adding
missing punctuation and capitalization.
src/configure: --enable-simulator deprecation warning

Warn in the --help output that --enable-simulator is deprecated.