further 11955 BF doc fixes & tidying
update download link in sidebar menu
Fix upgrade checker to delete loci_tools.jar when appropriate

If bioformats_package.jar is requested but loci_tools.jar is present,
then loci_tools.jar is deleted (so that only one jar is present).
Fix updater menu item to match window title
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.
Removing out of date version & milestone info
Merge pull request #900 from hflynn/11955-further

11955 further docs fixes
Merge pull request #908 from joshmoore/bftools-fix-again

Flatten path to bioformats_package.jar in bftools.zip (see gh-901)
Merge pull request #903 from melissalinkert/updater

Fix upgrade checker to delete loci_tools.jar when appropriate
Merge 'origin/dev_5_0' into deprecation

Conflicts:
	ant/toplevel.properties
	components/loci-plugins/src/plugins.config
	docs/sphinx/users/imagej/features.txt
	docs/sphinx/users/imagej/index.txt
	docs/sphinx/users/imagej/installing.txt
	docs/sphinx/users/imagej/load-images.txt