Merge pull request #452 from melissalinkert/autogen-deps

Fix classpath issues in the autogen component
Remove OME-TIFF and OME-XML links and use model_doc extlinks instead
Fix the component retrieval methods in Index16ColorModel

Byte-swapping the values is not correct, and getRed(int), getGreen(int),
and getBlue(int) should normalize the return values to 0-255, as per the
Javadoc for ColorModel:

http://docs.oracle.com/javase/1.5.0/docs/api/java/awt/image/ColorModel.html#getRed(int)
Merge pull request #453 from sbesson/formats_doc

Fix OME Model documentation link in the plonematch layout
merge dev_4_4 -D org -I include -E exclude: PR 379 (Fix source code links moved to the scifio-tools foder)
merge dev_4_4 -D org -I include -E exclude: PR 456 (Fix the component retrieval methods in Index16ColorModel (rebased onto dev_4_4))