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).
Revert "Update POM version numbers to 5.0.0-rc2"

This reverts commit ceb3c487984ba48b210af85cfd97c65ed0f7a540.
Update last version number to 5.0.0-rc2
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.
Deprecate classes in scifio-devel (in favor of loci.common.*)
Update classes in loci-legacy to include changes from ome.scifio.*
Change usage of ome.scifio.* to loci.common.*
Finish updating for ome.scifio.* deprecation
Update build system files to point to loci-common

loci-legacy and scifio-devel are now deprecated.
Update developer documentation to point to loci-common instead of scifio-devel
Move MetadataStore, MetadataRetrieve, and related classes to ome.xml.meta

This adds a dependency on loci-common to ome-xml; I would not expect
this to cause a problem.

Wrapper classes with the old package names are kept and are not
deprecated at the moment.  With the exception of MetadataRoot and
OMEXMLMetadataRoot (which were not present in 4.4.x), the old package names
are still used across the board.  For IFormatReader etc., we're going to have
to choose between using only the old package names and using only the new
package names - things like 'MetadataStore getMetadataStore()' mean that
deprecating current signatures and adding new signatures for the new classes
is not really possible.
Remove the 'native' component

This component was not built by default, and only contained the
deprecated bf-itk plugin.
Fix Maven source generation to use new package names
Fix test compile errors
Completely remove scifio-devel and any references to it

This component was never formally released, so remove it instead of
deprecating.