further 11955 BF doc fixes & tidying
update download link in sidebar menu
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Removing out of date version & milestone info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 #13 from joshmoore/deprecation

ome-io/plugins removal
Fix 'ant' and 'maven' commands for tools/test-build
Fix a handful of doc issues and links
Use 'BF software...'
Remove LOCI mailing list
Fix domain.prefix
Fix library and header names for cppwrap
Rename the poi-loci jar to ome-poi

The component name (poi) is still the same though, as it's consistent
with the other fork names.
Rename loci-plugins to bio-formats-plugins
Remainder of jar file renamings and documentation link updates
Merge branch 'more-renaming' into deprecation
Fix usage of saveBytes in minimum_writer.cpp
Fix usage of SVN_REVISION in showinf.cpp
Remove call to setMetadataCollected(boolean)