Improve performance of includeonly with "maintain counters and references"

Improve performance of includeonly with "maintain counters and references"

First, we do not need to run bibtex/biber on the maintenance run, as
the necessary references will be generated on the includeonly run.

Second, exclude the master from DepTable in maintenance run, as the
master is re-checked in any case in the includeonly run, and as it will
always be detected as changed due to the \includeonly statement, which
will trigger a complete build.

More improvements to follow.