Added documentation for data storage conventions (and history)
Flows now automatically create their unique output directories
Added gitignore file to prevent flow data from appearing in repository
Commands now get stderr/stdout paths automatically at build time
tasks executed now capture stdout and stderr
minor: stderr path now shown in example gene predictor run
Added FlowInstanceValue and CommandBlueprint.get_param
Ongoing progress commit for first multi-tool flow definition loader
Made get_command() method respect multiple parents, added shell of set_instance_value(), drastic changes to FlowInstanceValue class
first version with STDOUT and STDERR definitions
removed redundant get_param() def
Made Flow.get_command() a recursive search
Added exec_dir attribute to Command class
Added EMERGENCE_EXAMPLE_DATA_ROOT to settings.common
Task runner now sets cwd = Task.exec_dir
Fixed indent levels, upload now uses settings file
Added -p (prefix) option to better control output
Moved exec_dir attribute from Command to Step class, added FlowInstanceValue class
Removed Flow.get_data_path() in favor of Flow.exec_dir
Fixed spelling error in variable name 'commmand', made CommandParam.prefix attribute nullable