Usage:
<mode> <input file> <outputfile>

Where <mode> is chosen from:

Process - process a document (converting to SciXML if necessary),
          and find the chemicals.
Data - find experimental data (NMR spectra etc.)
SAF - produce a Standoff Annotation Format file

<mode> <directory>		

Import - imports a directory into your workspace
ProcessInWorkspace - works on directory heirarchies in the format generated by Import
ImportAndProcess - imports a directory, then parses the files in it

<mode> <input directory> <output directory>		

ProcessInto - creates an output directory based on an input directory
CrossProcess - see the documentation for more details

<mode> <modelname>

MakeModel - Turns the contents of your scrapbook into a new model in the
            models directory of your workspace

<mode>		

Server - start the server, configuring if necessary
ReConfigureServer - reconfigures the Oscar3 server
SortProps - sorts the Properties file