This requires some explanation: turns out, Ninja uses the $builddir
variable declared in the top-level Ninja file to figure out where the
command log should go. This resulted in a loss of incrementality between
the manual Ninja invocation in test_null_build_after_docs because they
used different Ninja files and therefore different values of $builddir.
The reason why this was not a problem before is that the output files of
the main Ninja file and the bootstrap one were separate, but with that
changing, this will start to matter.
Test: Presubmits.
Change-Id: I28959cc7d659e698c7694a58326c8731eac060eb