Remove classes and methods deprecated in 4.4.x

Conflicts:

	ant/toplevel.properties
	components/scifio/src/loci/formats/ome/OmeisException.java
	components/scifio/src/loci/formats/ome/OmeisImporter.java
Move turbojpeg component to the forks directory
Rename the scifio-tools component to bio-formats-tools
Remove obsolete omeul scripts
Update variable names in command line tool scripts
Rename the loci-common component to common
Move the Maven assembly components to the bundles directory
Fix a few outdated URLs and email addresses
Rename pom-scifio to pom-bio-formats

Conflicts:

	components/autogen/pom.xml
	components/bio-formats-tools/pom.xml
	components/bio-formats/pom.xml
	components/bundles/bioformats_package/pom.xml
	components/bundles/loci-tools/pom.xml
	components/bundles/ome-tools/pom.xml
	components/common/pom.xml
	components/forks/jai/pom.xml
	components/forks/mdbtools/pom.xml
	components/forks/poi/pom.xml
	components/forks/turbojpeg/pom.xml
	components/loci-plugins/pom.xml
	components/metakit/pom.xml
	components/ome-io/pom.xml
	components/ome-plugins/pom.xml
	components/ome-xml/pom.xml
	components/scifio/pom.xml
	components/specification/pom.xml
	components/stubs/lwf-stubs/pom.xml
	components/test-suite/pom.xml
	components/xsd-fu/pom.xml
	pom.xml

Conflicts:

	components/autogen/pom.xml
	components/bio-formats-tools/pom.xml
	components/bio-formats/pom.xml
	components/bundles/bioformats_package/pom.xml
	components/bundles/loci-tools/pom.xml
	components/bundles/ome-tools/pom.xml
	components/common/pom.xml
	components/forks/jai/pom.xml
	components/forks/mdbtools/pom.xml
	components/forks/poi/pom.xml
	components/forks/turbojpeg/pom.xml
	components/loci-plugins/pom.xml
	components/metakit/pom.xml
	components/ome-io/pom.xml
	components/ome-plugins/pom.xml
	components/ome-xml/pom.xml
	components/scifio/pom.xml
	components/specification/pom.xml
	components/stubs/lwf-stubs/pom.xml
	components/test-suite/pom.xml
	components/xsd-fu/pom.xml
	pom.xml
Simple move of scifio to impl-bsd
Minor impl-bsd changes
Fix whitespace
Start renaming scifio targets to impl-bsd
Move bio-formats to formats-gpl and impl-bsd to formats-bsd
Move relevant classes from formats-bsd to formats-api and update docs

Conflicts:

	components/formats-bsd/src/loci/formats/itk/ITKBridgePipes.java
Remove scan-deps.pl

This script is known to be not entirely accurate, and the information it
provides can be more easily and reliably produced by Maven.
Finish fixing header names and documentation links

Conflicts:

	components/common/src/loci/common/services/OMENotesService.java
	components/formats-bsd/src/loci/formats/ResourceNamer.java
	docs/sphinx/developers/xsd-fu.txt
	license/loci-legacy/license.txt
Rename ImageJ plugins menu item, and update docs and comments accordingly

Conflicts:

	components/loci-plugins/src/loci/plugins/macro/LociFunctions.java
	components/loci-plugins/src/plugins.config
	docs/sphinx/users/imagej/features.txt
	docs/sphinx/users/imagej/index.txt
Update a few more links to classes that have moved
ome-java: remove jar