Finished port for arachnid 0.0.1
change_default converts list to optlist (same with creating an option)
Added map_module_to_program to ensure the program added to the top of a configuration file is correct
Shortened input file names with commonprefix and fix a bug such that the correct script is in the header of a configuration file
Added ability to detect MPI implementation type to fill an empty command, also prioritized input parameters
Added automatic enhancement to last round of refinement
Updated parameters in project, added --scatter-doc and added automatic scattering file download for ribosomes
Added ability to write out workflow scripts
Added more robust import for associated shared library modules
Fixed file paths, now assumes script are run from project directory
Expanded documentation, fixed contents and first draft of reconstruction protocol
Added discussion group link
Added background and important links
Added template with javascript that scrolls the sidebar with the document
Fixed local variance calculation - similar to EMAN now
Reorganized documentation, rst files in docs now. Fixed layout in resources/template. Added templates in resources/template. Updated MANIFEST to reflect new source files
Updated install docs and moved css to external file
Fixed the external CSS to work properly with sphinx and updated the attribution and index pages
Fixed the CSS layout and updated the intro in index and readme
Fixed width of modules page