further 11955 BF doc fixes & tidying
update download link in sidebar menu
Add ome-io and ome-java jars to bioformats_package.jar
sorting index and installation guide
Further tidying from Roger
Flatten path to bioformats_package.jar in bftools.zip (see gh-901)

Since this uses the native zip command, invoking from the
artifact.dir seems to be the most portable way to get the
unprefixed jar into the zip.
Fix logback.xml XML header

`mvn` without this commit complained about
the logback.xml file (loudly).
Removing out of date version & milestone info
merge dev_5_0 -D org -I include -E exclude: PR 900 (11955 further docs fixes)
merge dev_5_0 -D org -I include -E exclude: PR 903 (Fix upgrade checker to delete loci_tools.jar when appropriate)
merge dev_5_0 -D org -I include -E exclude: PR 905 (Revert "Update POM version numbers to 5.0.0-rc2")
merge dev_5_0 -D org -I include -E exclude: PR 908 (Flatten path to bioformats_package.jar in bftools.zip (see gh-901))
merge dev_5_0 -D org -I include -E exclude: PR 909 (Add ome-io and ome-java jars to bioformats_package.jar)
merge dev_5_0 -D org -I include -E exclude: PR 912 (Fix logback.xml XML header)