Merge pull request #2087 from RosettaCommons/vmullig/fix_silent_read_issue_2
Incremental merge for fixing the silent file read issues
This is an initial merge of the changes in pull request #1955. It fixes the silent file read issues, but not the write issues. See that pull request for full details.
A handful of integration tests show cosmetic changes because the silent file reader is a bit more verbose with badly-formatted silent files, but no test changes of substance are observed. This should make silent file read much more resilient to the mysterious silent file write errors. Merging.