Use commons-io api that does not exclude dirs.
Revert "Add --wait to the test command inside the bundle archetype's metadata.xml."

This reverts commit d3fddd4df3dbc42354dc6bd1ae085e74353998da.
Merge pull request #117 from SeqWare/feature/arch-wait

Revert "Add --wait to the test command inside the bundle archetype's met...
Stop getting "help" from commons-io.
Merge pull request #116 from SeqWare/feature/bundle-conf

Feature/bundle conf
Allow input files to have merge rather than replace in the web service

Means the workflow status checker will not overwrite input files with blank
Disallow launch-scheduled with wait which doesn't make sense and isn't tested
Allow optionally listing workflows as TSV.
Remove deletion of input files from corresponding test
Stuff
Merge pull request #118 from SeqWare/feature/SEQWARE_1750_input_file_overwrite

Feature/seqware 1750 input file overwrite
Pre-process workflows to prevent names that cannot safely be used as parts of a filename.
Reduce unhelpful messaging.
Add missing new file.
Working prototype with orphan checking
Iterate version numbers
Update docs
Merge pull request #119 from SeqWare/feature/SEQWARE-1755

Feature/seqware 1755
Merge pull request #120 from SeqWare/feature/SEQWARE-1756

Allow optionally listing workflows as TSV.
Merge pull request #121 from SeqWare/feature/SEQWARE-1757

Reduce unhelpful messaging.