Rebase of checksum work onto develop

[bpindelski]

This PR is a manual rebase of #788, #827 and #897 onto develop, sprinkled with a couple of extra commits accommodating the differences caused by FS work and a cherry-pick of two commits by @mtbc from #890.

The server builds fine and imports images ok. /build.py -f components/common/build.xml clean install test-compile integration doesn't fail. The Spring context wiring would need a second pair of eyes to look at (no startup errors though).

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-merge-develop#193. See the console output for more details.

[bpindelski]

This doesn't merge well with #881 still open. I will have to wait till that one goes into develop and then rebase. Also noticed that 5a2f588 is quite fishy, as it duplicates entries in beanRefContext.xml, so will have to fix that.

[bpindelski]

Good to review, once #881 goes in. It had a missing commit from #788 but all fixed now.

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-merge-develop#194. See the console output for more details.

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-merge-develop#195. See the console output for more details.

[joshmoore]

You should be able to merge in develop or rebase now, @bpindelski.

[joshmoore]

Importing and setting in originalfile table all looks correct. None of the Spring configuration files looks obviously wrong. Both Indexer and PixelData have started up correctly (which is usually what I break when working with the Spring files). As a rebase, this looks great. Merging.