Removed Javadoc warnings

Cleaned up all javadoc so that running "mvn javadoc:javadoc" completes
without any warnings, and Eclipse is free of any "javadoc:" warnings.
Remove compiler warnings

Updated source code to remove as many warnings as seemed reasonable
based on the ImageJ2/LOCI Eclipse configuration.

Some will likely always remain, such as resources not being closed, as
there are legitimate places where those resources should not be closed.