Fix a handful of missed broken links
Use the full path to the utils directory in the docs

I thought using :source: would work so that the branch name wouldn't
have to be hard-coded, but evidently that causes the build to fail.
merge dev_5_0 -D org -I include -E exclude: PR 911 (Remove, rename, and/or deprecate relevant classes)
merge dev_5_0 -D org -I include -E exclude: PR 918 (source-archive supports openmicroscopy source releases)