Log remaining UnsupportedEncodingExceptions
Update links in readme, LOCI-plugin & ImageViewer
Fixing imagej & itk links
Fixing links to imagej plugins
Tidying and consistency editing
Remove old Bio-Formats logos

These aren't referenced anywhere in the codebase, and are superceded by
new logos stored elsewhere.
Update remaining logos to latest versions
Ignore two types of bugs in the loci.common package

These bugs are flagged as a result of the 'equals(Object)'
implementations and the fact that some loci.common.* classes extend
the same class name in ome.scifio.*.

This is generally bad practice, but in this specific case it is the
intended behavior and I don't see a good way around it.
Fix implementation of CoreMetadata.clone()

This means that clone() should work correctly if CoreMetadata is ever
subclassed.

I assume that this is safe thing to do based upon this section of the
Javadoc
(http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html#clone()):

"The method clone for class Object performs a specific cloning
operation. First, if the class of this object does not implement the
interface Cloneable, then a CloneNotSupportedException is thrown. Note
that all arrays are considered to implement the interface Cloneable.
Otherwise, this method creates a new instance of the class of this
object and initializes all its fields with exactly the contents of the
corresponding fields of this object, as if by assignment; the contents
of the fields are not themselves cloned."

...which to me reads as though 'super.clone()' will do exactly what 'new
CoreMetadata(this)' is doing.
Merge pull request #300 from hflynn/newdoc_fixes_develop

Update web links & logos develop
Fix the "bftools.files" property to match the contents of tools/
LIFReader: Add User-Comment tags to the series metadata
Merge pull request #297 from melissalinkert/writer-tests

Writer tests
Merge pull request #298 from melissalinkert/valid-ome-xml-develop

Write valid OME-XML files
Merge pull request #299 from melissalinkert/findbugs-fixes-develop

Findbugs fixes
Merge pull request #302 from melissalinkert/dist-bftools

Fix the "bftools.files" property to match the contents of tools/
XMLTools: sanitizeXML does not strip newlines
Removed benchmark from native component

The JNI and Jace implementations of BF-ITK are being removed. Thus there
is no need to benchmark and compare them any more.
Removed BF-ITK-Jace project

The bf-itk-pipes implementation will be the supported BF-ITK plug-in
now. The Jace implementation is outdated and unsupported, thus it is
being removed.
Removed BF-ITK-JNI project

The bf-itk-pipes implementation is now the supported BF-ITK
implementation.

The ITKBridgeJNI class was causing findbugs issues. This implementation
is outdated and not fully functional, therefore instead of attempting to
support multiple implementations for BF-ITK, the JNI implementation will
be removed.