Data tests: allow directories to be specified via a file
Merge pull request #138 from melissalinkert/data-test-updates

Data tests: allow directories to be specified via a file
Be consistent with test target properties
Migrate loci.common to scifio-devel component

Classes have been migrated to ome.scifio.common, ome.scifio.io and
ome.scifio.xml packages.

Unit tests have been similarly migrated based on function.

Build files for both Ant and Maven have been updated accordingly.
Update package.html documentation
Update license headers for moved files
Removed loci-common.jar from loci tools deps

As the loci-common jar was absorbed into SCIFIO, it has been removed
from the loci tools dependency list in the ant toplevel.properties file.
Removed ant references to common targets

Removed all references to compile/jar/clean/etc... common from ant
targets.

These targets now depend on scifio if they did not already, as the
common classes migrated there.
Updated ome-notes dependencies to jar-xxxx

Updated the ome-notes dependencies to point to jar- targets instead of
compile- targets.
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 Loci-Legacy

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

Loci-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 Loci-legacy component. This will ensure
that the delegator classes will have the same history as the original
classes.
Added loci-legacy component

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

All loci.common classes within the loci-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
loci-legacy fully functional.

Conflicts:

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

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