Merge pull request #961 from melissalinkert/rebased/develop/5.0.0-autogen

Update autogen scripts and templates for restructuring (rebased onto develop)
Merge pull request #954 from melissalinkert/rebased/develop/aperio-links

Fix ImageScope links to match the committed documentation (rebased onto develop)
Merge pull request #956 from sbesson/rebased/develop/5-release

Final BF doc updates for 5 release (rebased onto develop)
Update develop submodules

Repository: openmicroscopy/bioformats
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