scan method improvements
Removed usage of project.config. Moved code to get genome and annotation in cli.utils
Fixed single_end, genome and annotation default value. Added name to return values from find_secondary.
Fixed abslute path issue in make_link. Added import_dataset method.
Fixed test failure for name in find_secondary return values
Creating new project and importing datasets when calling grape run without a project.
Added execution command line parameters to run and submit commands
Separate group for pipeline execution parameters
Added support for relative paths in csv/tsv file
Fixed some issues when running with no pre-initialized project
Fixed issue with md5 if file does not exist
Project initialization
Merge branch 'master' into thasso
Merge branch 'develop' into thasso

Conflicts:
	grape/index.py
Added project scanning
Added index validation
Added --force option to pipeline runs
empty lines are so nice
Added json export
Delete old index module