Bioprov

* Patch file deserializer bug [x]

* Add more database methods [x]
* Improver error handling for JSON methods [x]
* Add Project.run_programs method [x]
* Create ProvEntity and ProvActivity for Project.files and .programs [x]
* Create Project Bundle for .files and .programs [x]

* Update README [x]
* Add Project.add_files() and add_programs() method [x]
* Improve Project deserializer [x]
* Add Project steps to Workflow class [x]

* Improve Sample.to_series() and Project.to_csv() methods [x]
* Add Project.to_csv() calls to tests [x]
* Add database commands to CLI options [x]
* Remodel environment as Agent rather than Entity [x]
* Improve output PROVN documents [x]
* Add Diamond preset and tests [x]

* Add blastdb example data [x]
* Add BLASTn preset and workflow and respective tests [x]
* Improve BioProvDB tests [x]
* Improve Project.auto_update and Project.sha1 behaviour and tests [x]
* Improve Workflow behaviour for custom Workflow arguments [x]

* Add BioProvDB class [x]
* Add database methods to Project class [x]
* Add BioProvDB tests [x]
* Add dot attribute to BioProvDocument [x]
* Update W3C-PROV tutorial [x]
* Improve test coverage [x]
* Debug Program deserializer [x]