Fix stupid byte-order mark issue and some progress on workflow run conventions checking


Former-commit-id: b8d77ddf83a5f20c8aadbebcd066228b491a9193
Archiving Morgan's useful DB diagrams


Former-commit-id: 0e83b2c49d048f5f0b3ed35e55ee9febdfa19833
Merge pull request #122 from SeqWare/feature/status-host

Add --host option to propagate-statuses. Skip host check in WorkflowStat...

Former-commit-id: 19a2fd91fd4fc52179924f03e9c2638c8650340c
Fix typo in doc.

Former-commit-id: 93f1d1eb216675fc46c625f98a4e1c32fe20c813
Initial work on Samplehierarchy


Former-commit-id: bf5bda54b3eb54620364dc6aa62603d74c1063fd
Update docs and tweak new CLI.

Former-commit-id: 8dc87bbb09a748b2dc82b001566b8e3510d4c09b
Update new CLI: bundle test applies to entire bundle or specified workflow, always uses 'test' node value from metadata.xml.  bundle dry-run and bundle launch allow for fully specified launching (i.e., not using the 'test' node value).

Former-commit-id: bb1ec777b24a1cf30a3213e8a7df59ae82d78820
Comment archetype-catalog.xml with brief usage instructions.

Former-commit-id: ac726d5f2df1062fcdb29a72b98e2b91dbfaebd7
Add bundle validation immediately prior to packaging.

Former-commit-id: d50385afe4c13f1e6397f423d62bb3ade199b957
Remove `bundle test` entirely.  `bundle dry-run` and `bundle launch` are sufficient and less complex.

Former-commit-id: 6fc375adf50c2888ff53b162ef985e6637e4183f
Functions to obtain bundle info.

Former-commit-id: 42cb1c3ae03663f002883d27dd9b70f9f9a6fbe3
Make ini optional for `bundle dry-run` and `bundle launch`, defaulting to the config value defined in metadata.xml.

Former-commit-id: 5dd49693f8500edb09174a66c869721983b9d102
Sample hierarchy and duplicate attribute keys


Former-commit-id: 5cc5801b090e949484953fe155273f18accd9c28
Functions to obtain the config path.

Former-commit-id: 4004411e72d7f80d7d1f3f24e15fdfc2e321a263
Update docs to reflect new testing commands.

Former-commit-id: a0aabae5ffebc3113f95e782c9d62b0bd55298cf
Clarify how default engine is picked.

Former-commit-id: b0c39a74201c936ddb36cd81e3c4430353b91a2e
Add better messaging to oozie --wait, and return non-zero exit code when run fails.

Former-commit-id: 9392194fa5c34af92489bc075f3b256cd2dcc8d6
Expose source file of BundleInfo

Former-commit-id: b7ac9859f556d12fd0d28c4abf316585b6aedbf2
Make new CLI smarter when dealing with bundle.

Former-commit-id: e2291cdecad5e2f7b7195dab8f80c9eb3ac774ca
Resolve ini files and ensure they exist before invoking WorkflowLauncher.

Former-commit-id: d06ceeca75b18bd93e90e98f0de448ebec69cabf