Unify .ninja_log files

Having separate .ninja_log files doesn't work very well after
https://github.com/ninja-build/ninja/commit/04d886b11041bb59d01df794cce7a1e8cad2250d
since the last successful timestamp is not recorded in the ninja log.
This was triggering the primary builder to be run twice on every build
since it was always considered out of date in the primary, then main
stages.

The two bootstrap stages already were unified when minibootstrap was
simplified, but this combines the main stage as well. This means that
we'll save some time running globs that are shared between minibp and
the primary builder as well (subdirs globs).

The cleanup code needed to be refactored, since the ninja_log will have
entries from the main stage as well. So instead of looking at everything
in the ninja log, take a string prefix to limit what we may clean.

Change-Id: I8d43168643aa8a0c6c3e48c6101eaa45d174bbe5