- Can't have the b.txt in first text be temp and expect it present, it
will correctly be deleted.
- Add third MRE which is targeting more of a log issue

The main scheduler loop terminates if there are no more runnable
jobs. This tests if there still are jobs that should be run, but that
we cannot seem to get to. If so, print an error message, print the
files affected, and exit 1. The latter is important so Snakemake can,
as hotfix, be rerun in a loop until it's actually completed all
tasks.

The aggressive early deletion of temp files must ignore
checkpoints. Other rules depend on a checkpoint only via the first
output file of the checkpoint (flagged string) as a stub. All other
outputs marked as temp would be deleted (and have been before this
patch). Since those files are missing, the dependent rules will never
be runnable and the workflow ends before all targets have been built.