Added a simpler parsing function for classes implementing ParserInterface. This function does not expect command line arguments that can come from external programs running the parser.

Flexiable recorder/parser functions added to SmartParser, Stream RTF, PAR, CRD, COOR readers and force field parameters with ParmEd support added to MDDataAccess, resetting support added to MetaInfoStorage.

3dbeda49095faf438840110e9b6e3fccd06a1aef -- Allowed the usage of schemes other than nmd:// in the JSON files. This allows testing with files generated on a local machine.
f689e878a4775b1c4a06a70e5aabbaf2d42be25c -- return code-specific section (named '^x_.*_section.*') as ArchiveSectionJSON
e24727f9a67462d59c5a580888edbc73ac131aeb -- comment on code-specific x_*_section
be56a3083cf035ea0d7d53946581ee1ac4c9e0b4 -- fix repeating-values issue in archive.py (instead of N actual values, N times the first value was returned when looking up indices)
ae7880e302553768a40fa16cef06b848ca33359d -- moved reading mainfile_uri to archiveiterator
75f571c6c99c5377da46b6f56e276689327dfa6e -- Added pid to mongodb. Fixed tests for db changes. Fixed schema and postprocessor for empty pids and repository download uris.