Remove some unused args from Blueprint.

These are: TopFile and GeneratingPrimaryBuilder.

Also re-shuffle the list of flags to make a bit more sense and finish
the rename of BuildDir and NinjaBuildDir to SoongOutDir and OutDir,
respectively.

Test: Presubmits.
Change-Id: I103ff5f09f1c0d16f695a7da5dea13b55028e33e