Some doc clarifications.
#768, #478: Input modules doc clarification
#610: More revision
Typo + doc edit
#716: Added # of digits for numbering
Correcting some misleading help text
#643: Corrected,added distance measures
#768: Added example
Error if data has NaNs + display window
added alternative shortcut file
took out unnecessary output in Makefile
Fixed URL for matplotlib
killed splash box in cellprofiler shortcut
issue #771 added JNI NewString wrapper + tests & usage in arg processing and OMEXML metadata processing
Was only reading series #0. Tried to read series #1 for flex and found out that reader in load_using_bioformats needed setGroupFiles(False) in order to be consistent with get_omexml_metadata
Added JB_Env.get_string + test
Fix problems displaying CorrectIllumination_Calculate during analysis
issue #769 adjust to new signature of OMEXMLService.createOMEXMLRoot for no good reason