Require ninja 1.6.0, remove workaround

The workaround no longer works with the new stage selector. We may run
bootstrap.ninja.in twice before running the next stage, but we can't
encode whether to run another ninja instance in the checked in
build.ninja.in.

This can likely be solved, but now that there's an official release with
support for multiple passes, just push up the required version.

Change-Id: I76e321912e323d60e462aabec61bdfcc7118cd5e