Keep temp() output of checkpoint (see snakemake#823)

The output of checkpoint rules may be needed by other rules, which, at this point have not had a chance to add their file requirements to their depending list.

snakemake/dag.py

@@ -617,7 +617,7 @@ def unneeded_files():
                 yield from filterfalse(partial(needed, job_), tempfiles & files)
 
             # temp output
-            if not job.dynamic_output and (
+            if not job.dynamic_output and not job.is_checkpoint (
                 job not in self.targetjobs or job.rule.name == self.workflow.first_rule
             ):
                 tempfiles = (