Prevent fragile use cases of checkpoint appending

Prevent fragile use cases of checkpoint appending

There are way too many ways we allow runs to be continued
and extended. We still allow the checkpoint file to be
missing (so -cpi can be used for all command lines), but
we warn if it is not found. To avoid mistakes with file
appending when restarting from checkpoints, we now require
that all previous output files must be present
(unless -noappend is used), and that the file names must
match the ones used in the previous run.

Fixes #1777.

Change-Id: Id9e89773a4a9214be6dbb76676c526e98e12bd37