Tweak editor for input slot values.
Merge branch 'master' of https://bitbucket.org/campagnelaboratory/nyosh
Add gobyweb.interactive.reads language. The language offers a tool to pre-process input reads and creates GobyWeb samples. Only the structure and editor of the tool are implemented. Also, add JobRef and JobRefSet to gobyweb.interactive.
First working version of ProcessReadsTool (still need to manage samples composed by multiple reads files). Add a synchronized version of the FileSet instance registration. Use this version to register the merge plan.
Parse the sample definition file in ProcessReadsTool and create the sample list.
Run the ExecutionTool on paired samples according to the definitions provided in the TSV within the ProcessReadsTool. The tool is now fully functional and looks working on test data.
Watch the indenting: it does matter in a plugin build script. Make sure genome language is part of Interactive plugin. Increment plugin version to 2.0.6. Only the Interactive plugin is affected.
Handle the case when no sample file matches the sample definition.
Add intention for renaming fileset instances in reads language.
Change ProcessReadsTool to use the new PROCESS_PAIRED_READS_TASK plugin. Remove reads language from devkit.
Modify assemble scripts to work also with jenkins
Further changes to assemble scripts to work  with jenkins
Add QueriesGenerated.java for lib/generator. Modify gitignore to accept it.
Add QueriesGenerated.class for lib/generator. Modify gitignore to accept it.
Ignore generation errors before assembling the plugins
Ignore generation errors.
Deploy XChart plugin before assembling the plugins
Fix MPS plugins home path
Add QueriesGenerated class and source for gobyweb/generator.
Add QueriesGenerated class and source for environment/generator.