Fix classpath issues in the autogen component

Conflicts:

	components/autogen/pom.xml
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 444 (ScanR: fix well linkage issues)
merge dev_4_4 -D org -I include -E exclude: PR 445 (TIFF: correct for invalid tile heights)
merge dev_4_4 -D org -I include -E exclude: PR 450 (Trestle: fix optimal tile sizes for subresolutions (rebased onto dev_4_4))
merge dev_4_4 -D org -I include -E exclude: PR 452 (Fix classpath issues in the autogen component)