Removed loci-common from Maven references

Updated all poms with a dependency on loci-common. If a project that
depended on loci-common did not previously depend on scifio, a scifio
dependency was added.
Updated build.properties to remove loci-common.jar

As loci-common was migrated into SCIFIO, there is no more loci-common
jar. If a project that depended on loci-common did not previously have a
scifio dependency, that project now depends on scifio.jar.

Cherry-pick Conflicts:

	components/autogen/build.properties
Updated showinf dependency on loci-common

Removed the loci-common include in showinf.cpp and updated package
reference from loci.common to ome.scifio.
Removed loci-common ref in LibraryChecker

LibraryChecker now looks for RandomAccessInputStream in the
ome.scifio.io package of the scifio.jar instead of loci-common.
Removed loci-common ref from ome-tools

The assembly.xml in ome-tools referenced the loci-common jar. This has
been removed.
Initial copy of loci.common to BF-Legacy

This is the first of 2 commits to preserve backwards compatibility with
the legacy loci.common package.

Bio-formats-legacy is not in a functional state with this commit. It is
simply a copy, with no changes, of all loci.common classes from the
scifio component to the bio-formats-legacy component. This will ensure
that the delegator classes will have the same history as the original
classes.
Added bio-formats-legacy component

This is the second in 2 commits to preserve backwards compatibility
within the loci.common packages.

all loci.common classes within the bio-formats-legacy component have
been converted to delegator classes, which pass functionality to the
maintained ome.scifio equivalents.

This change ialso includes maven and ant targets, making
bio-formats-legacy fully functional.

Conflicts:

	components/bio-formats-legacy/src/loci/common/AbstractNIOHandle.java
	components/bio-formats-legacy/src/loci/common/BZip2Handle.java
	components/bio-formats-legacy/src/loci/common/ByteArrayHandle.java
	components/bio-formats-legacy/src/loci/common/CBZip2InputStream.java
	components/bio-formats-legacy/src/loci/common/CRC.java
	components/bio-formats-legacy/src/loci/common/Constants.java
	components/bio-formats-legacy/src/loci/common/DataTools.java
	components/bio-formats-legacy/src/loci/common/DateTools.java
	components/bio-formats-legacy/src/loci/common/DebugTools.java
	components/bio-formats-legacy/src/loci/common/FileHandle.java
	components/bio-formats-legacy/src/loci/common/GZipHandle.java
	components/bio-formats-legacy/src/loci/common/HandleException.java
	components/bio-formats-legacy/src/loci/common/IRandomAccess.java
	components/bio-formats-legacy/src/loci/common/IniList.java
	components/bio-formats-legacy/src/loci/common/IniParser.java
	components/bio-formats-legacy/src/loci/common/IniTable.java
	components/bio-formats-legacy/src/loci/common/IniWriter.java
	components/bio-formats-legacy/src/loci/common/Location.java
	components/bio-formats-legacy/src/loci/common/NIOByteBufferProvider.java
	components/bio-formats-legacy/src/loci/common/NIOFileHandle.java
	components/bio-formats-legacy/src/loci/common/NIOInputStream.java
	components/bio-formats-legacy/src/loci/common/RandomAccessInputStream.java
	components/bio-formats-legacy/src/loci/common/RandomAccessOutputStream.java
	components/bio-formats-legacy/src/loci/common/ReflectException.java
	components/bio-formats-legacy/src/loci/common/ReflectedUniverse.java
	components/bio-formats-legacy/src/loci/common/Region.java
	components/bio-formats-legacy/src/loci/common/StatusEvent.java
	components/bio-formats-legacy/src/loci/common/StatusListener.java
	components/bio-formats-legacy/src/loci/common/StatusReporter.java
	components/bio-formats-legacy/src/loci/common/StreamHandle.java
	components/bio-formats-legacy/src/loci/common/URLHandle.java
	components/bio-formats-legacy/src/loci/common/ZipHandle.java
	components/bio-formats-legacy/src/loci/common/enumeration/CodedEnum.java
	components/bio-formats-legacy/src/loci/common/enumeration/EnumException.java
	components/bio-formats-legacy/src/loci/common/services/AbstractService.java
	components/bio-formats-legacy/src/loci/common/services/DependencyException.java
	components/bio-formats-legacy/src/loci/common/services/OMENotesService.java
	components/bio-formats-legacy/src/loci/common/services/Service.java
	components/bio-formats-legacy/src/loci/common/services/ServiceException.java
	components/bio-formats-legacy/src/loci/common/services/ServiceFactory.java
	components/bio-formats-legacy/src/loci/common/xml/BaseHandler.java
	components/bio-formats-legacy/src/loci/common/xml/ParserErrorHandler.java
	components/bio-formats-legacy/src/loci/common/xml/ValidationErrorHandler.java
	components/bio-formats-legacy/src/loci/common/xml/XMLTools.java
Added bflegacy dependency to ome-notes

The ant and maven build systems for the ome-notes component have been
updated to include a dependency on the bio-formats-legacy component.
Added bflegacy ant target to tools bundle

The bio-formats-legacy jar will now be built as part of the ant tools
target.
Updated utils imports to ome.scifio.common

Utility classes in the scifio and test-suite componenets were still
referencing the deprecated loci.common package.

For projects in development such as these, the imports are updated to
ome.scifio.common (as opposed to using the delegators in the
bio-formats-legacy component)
Removed common component directory

With the bio-formats-legacy component fully functional and all
loci.common classes in development migrated to ome.scifio packages,
there is no need for the common component.
Removed utils-bflegacy target

The utils package in bio-formats-legacy is currently unused. Thus its
utils ant target and any associated references have been removed until
there is a need for them.
Fixed XsltProc import

The scifio util class XsltProc was referencing a non-existant package:
ome.scifio.common.xml. It has been corrected to ome.scifio.xml
Updated bio-formats utils imports

As these are actively developed classes, all the bio-formats utils
classes should depend on the ome.scifio common-equivalent classes
instead of loci.common.*.

These imports have been updated.
Updated doc.export loci.common imports

As bio-formats is an actively developed component, there should be no
references to the legacy loci.common packages.

The example classes in doc.export have been thusly updated to use the
refactored ome.scifio.* packages.
Added services.properties to scifio.jar

Updated SCIFIO's build.properties so that ant targets will include
services.properties in scifio.jar.
Added missing logging jars to loci-plugins

Updated the loci-plugins build.properties with necessary logging jars.
Set up CaseInsensitiveLocation delegation

Moved functional code to ome.scifio.io.CaseInsensitiveLocation

Updated loci.common.Location delegator to use a protected
ome.scifio.io.Location for delegation, to allow visibility for extending
classes (such as CaseInsensitiveLocation).

loci.common.CaseInsensitiveLocation now delegates to its ome.scifio.io
equivalent.
Removed remaining loci.common references

Removed loci.common imports, updating them with the latest scifio
imports, for Zeiss classes + IFD.