Use commons-io api that does not exclude dirs.

Former-commit-id: b48032e44de20514e869b7171dfe8ae33049b27a
Revert "Add --wait to the test command inside the bundle archetype's metadata.xml."

This reverts commit 33267c95f34c24f5b95d4fc3c16d583edcc945f5 [formerly d3fddd4df3dbc42354dc6bd1ae085e74353998da].


Former-commit-id: 15fa3c25d32dffd60a32276abb6956ac07a9e512
Merge pull request #117 from SeqWare/feature/arch-wait

Revert "Add --wait to the test command inside the bundle archetype's met...

Former-commit-id: ec1239fd47d8918c64a9296ccba5b3fffc4f27ff
Stop getting "help" from commons-io.

Former-commit-id: 50065dffc77dd02ccef189486e42aaa839965a94
Merge pull request #116 from SeqWare/feature/bundle-conf

Feature/bundle conf

Former-commit-id: 506a2d6d850de321520e01abc6f298321702bebd
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


Former-commit-id: 46a95e598dceafb86a0229aa02ce2cdfa44caa8e
Disallow launch-scheduled with wait which doesn't make sense and isn't tested


Former-commit-id: 84e6f8c8a777140421b738b372152db072085b56
Allow optionally listing workflows as TSV.

Former-commit-id: 1df1ee7e56b620797dcc6db6c31b6e62e4c412c4
Remove deletion of input files from corresponding test


Former-commit-id: 17862c35475c85b2794076d7eba7e8d40d64bf42
Stuff


Former-commit-id: 93d0c10302aa6af9cf4478bfe0caafd61a4af00c
Merge pull request #118 from SeqWare/feature/SEQWARE_1750_input_file_overwrite

Feature/seqware 1750 input file overwrite

Former-commit-id: ff0867a03848cefa247f665ac042f7f106c010ea
Pre-process workflows to prevent names that cannot safely be used as parts of a filename.

Former-commit-id: 07801425967fde147f7d8062848bd57e7abaf211
Reduce unhelpful messaging.

Former-commit-id: c7f5ac460e462c0825823563fdae74fb20cd2289
Add missing new file.

Former-commit-id: 775b8959c05e332f8fa4dd1c39389e33f97bada0
Working prototype with orphan checking


Former-commit-id: 9613dd45959d03ed774291eda8817e9b0a146738
Iterate version numbers


Former-commit-id: 3049ffd3448cee811396666143448d8b912ef684
Update docs


Former-commit-id: 9ac443ddfd9afd8153790196824adba7e675f17a
Merge pull request #119 from SeqWare/feature/SEQWARE-1755

Feature/seqware 1755

Former-commit-id: fa2368ce61b8a91a777307086872f06795d79966
Merge pull request #120 from SeqWare/feature/SEQWARE-1756

Allow optionally listing workflows as TSV.

Former-commit-id: 5019d814581554b37e19e18e33f6469b06570dc7
Merge pull request #121 from SeqWare/feature/SEQWARE-1757

Reduce unhelpful messaging.

Former-commit-id: fc9ccb994036036f8eb79f74fcf72a18dc7f05b2