Patch for CellProfiler issue 1043 - Cellomics files with renamed filenames
Deprecate classes in scifio-devel (in favor of loci.common.*)

Conflicts:

	components/loci-legacy/src/loci/common/adapter/CodedEnumAdapter.java
	components/loci-legacy/src/loci/common/adapter/IRandomAccessAdapter.java
	components/loci-legacy/src/loci/common/adapter/StatusListenerAdapter.java
	components/loci-legacy/src/loci/common/adapter/StatusReporterAdapter.java
	components/loci-legacy/src/loci/legacy/adapter/AbstractLegacyAdapter.java
	components/loci-legacy/src/loci/legacy/adapter/AdapterTools.java
	components/loci-legacy/src/loci/legacy/adapter/LegacyAdapter.java
	components/loci-legacy/src/loci/legacy/adapter/Wrapper.java
	components/loci-legacy/src/loci/utils/ProtectedMethodInvoker.java
	components/loci-legacy/test/loci/legacy/utests/LegacyAdapterTest.java
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.

Conflicts:

	components/scifio/build.xml
	components/xsd-fu/python/ome/modeltools/config.py
Remove the 'native' component

This component was not built by default, and only contained the
deprecated bf-itk plugin.

Conflicts:

	components/native/bf-itk/CMakeLists.txt
	components/native/bf-itk/LICENSE.txt
	components/native/bf-itk/itkBioFormatsIOPlugin.cxx
	components/native/bf-itk/itkBioFormatsIOPlugin.h
	components/native/bf-itk/itkBioFormatsIOWin32Header.h
	components/native/bf-itk/itkBioFormatsImageIO.cxx
	components/native/bf-itk/itkBioFormatsImageIO.h
	components/native/bf-itk/itkBioFormatsImageIOConfigure.h.in
	components/native/bf-itk/itkBioFormatsImageIOFactory.cxx
	components/native/bf-itk/itkBioFormatsImageIOFactory.h
	components/native/bf-itk/itkBioFormatsImageIOTest.cxx
	components/native/bf-itk/itkBioFormatsImageInfo.cxx
	components/native/bf-itk/itkRGBBioFormatsImageIOTest.cxx
	components/native/bf-itk/itkVectorImageBioFormatsImageIOTest.cxx
	components/native/bf-itk/perf.cxx
	components/native/bf-itk/pom.xml
	components/native/pom.xml
Fix Maven source generation to use new package names

Conflicts:

	components/scifio/pom.xml
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.

Conflicts:

	components/scifio-devel/LICENSE.txt
	components/scifio-devel/pom.xml
	components/scifio-devel/src/ome/scifio/common/CRC.java
	components/scifio-devel/src/ome/scifio/common/Constants.java
	components/scifio-devel/src/ome/scifio/common/DataTools.java
	components/scifio-devel/src/ome/scifio/common/DateTools.java
	components/scifio-devel/src/ome/scifio/common/DebugTools.java
	components/scifio-devel/src/ome/scifio/common/IniList.java
	components/scifio-devel/src/ome/scifio/common/IniParser.java
	components/scifio-devel/src/ome/scifio/common/IniTable.java
	components/scifio-devel/src/ome/scifio/common/IniWriter.java
	components/scifio-devel/src/ome/scifio/common/Log4jTools.java
	components/scifio-devel/src/ome/scifio/common/LogbackTools.java
	components/scifio-devel/src/ome/scifio/common/ReflectException.java
	components/scifio-devel/src/ome/scifio/common/ReflectedUniverse.java
	components/scifio-devel/src/ome/scifio/common/Region.java
	components/scifio-devel/src/ome/scifio/common/StatusEvent.java
	components/scifio-devel/src/ome/scifio/common/StatusListener.java
	components/scifio-devel/src/ome/scifio/common/StatusReporter.java
	components/scifio-devel/src/ome/scifio/common/package.html
	components/scifio-devel/src/ome/scifio/enumeration/CodedEnum.java
	components/scifio-devel/src/ome/scifio/enumeration/EnumException.java
	components/scifio-devel/src/ome/scifio/io/AbstractNIOHandle.java
	components/scifio-devel/src/ome/scifio/io/BZip2Handle.java
	components/scifio-devel/src/ome/scifio/io/ByteArrayHandle.java
	components/scifio-devel/src/ome/scifio/io/CBZip2InputStream.java
	components/scifio-devel/src/ome/scifio/io/CaseInsensitiveLocation.java
	components/scifio-devel/src/ome/scifio/io/FileHandle.java
	components/scifio-devel/src/ome/scifio/io/GZipHandle.java
	components/scifio-devel/src/ome/scifio/io/HandleException.java
	components/scifio-devel/src/ome/scifio/io/IRandomAccess.java
	components/scifio-devel/src/ome/scifio/io/Location.java
	components/scifio-devel/src/ome/scifio/io/NIOByteBufferProvider.java
	components/scifio-devel/src/ome/scifio/io/NIOFileHandle.java
	components/scifio-devel/src/ome/scifio/io/NIOInputStream.java
	components/scifio-devel/src/ome/scifio/io/RandomAccessInputStream.java
	components/scifio-devel/src/ome/scifio/io/RandomAccessOutputStream.java
	components/scifio-devel/src/ome/scifio/io/StreamHandle.java
	components/scifio-devel/src/ome/scifio/io/URLHandle.java
	components/scifio-devel/src/ome/scifio/io/ZipHandle.java
	components/scifio-devel/src/ome/scifio/xml/BaseHandler.java
	components/scifio-devel/src/ome/scifio/xml/MetadataHandler.java
	components/scifio-devel/src/ome/scifio/xml/ParserErrorHandler.java
	components/scifio-devel/src/ome/scifio/xml/ValidationErrorHandler.java
	components/scifio-devel/src/ome/scifio/xml/ValidationSAXHandler.java
	components/scifio-devel/src/ome/scifio/xml/XMLTools.java
	components/scifio-devel/test/ome/scifio/common/utests/DataToolsTest.java
	components/scifio-devel/test/ome/scifio/common/utests/EncodingTest.java
	components/scifio-devel/test/ome/scifio/io/utests/BufferAlignmentReadTest.java
	components/scifio-devel/test/ome/scifio/io/utests/BufferAlignmentWriteTest.java
	components/scifio-devel/test/ome/scifio/io/utests/EndiannessTest.java
	components/scifio-devel/test/ome/scifio/io/utests/LocationTest.java
	components/scifio-devel/test/ome/scifio/io/utests/RandomAccessInputStreamTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadByteArrayTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadByteBufferTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadByteSubArrayTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadByteTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadCharTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadDoubleTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadFloatTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadIntTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadLineTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadLongTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadOnlyTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadShortTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadUnsignedByteTest.java
	components/scifio-devel/test/ome/scifio/io/utests/ReadUnsignedShortTest.java
	components/scifio-devel/test/ome/scifio/io/utests/SkipBytesTest.java
	components/scifio-devel/test/ome/scifio/io/utests/TypeDetectionTest.java
	components/scifio-devel/test/ome/scifio/io/utests/URLHandleTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteByteArrayTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteByteBufferTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteByteTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteBytesTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteCharTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteCharsTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteDoubleTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteFloatTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteIntTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteLongTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteShortTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteUTFTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteUnsignedByteTest.java
	components/scifio-devel/test/ome/scifio/io/utests/WriteUnsignedShortTest.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/BZip2HandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/ByteArrayHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/ExistingByteArrayHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/GZipHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/IRandomAccessProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/IRandomAccessProviderFactory.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/NIOFileHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/NewByteArrayHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/URLHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/providers/ZipHandleProvider.java
	components/scifio-devel/test/ome/scifio/io/utests/testng-template.xml
	components/scifio-devel/utils/ReflectionPerformance.java
	components/scifio-devel/utils/XsltProc.java
Remove loci-legacy component and references to it

This component was never formally released, and is replaced by
loci-common.

Conflicts:

	components/loci-legacy/LICENSE.txt
	components/loci-legacy/pom.xml
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