Kepler

I fixed a few files in the ptII tree that had the problem of missing
empty lines in the copyright.

$PTII/adm/copyright/chkcopyright was enhanced to check for this problem.
Note that to run this script properly under non-Windows platforms,
the Java files should not have control-ms in them.

Currently, the files that might have problems are:

bash-3.2$ find . -name "*.java" > /tmp/kj
bash-3.2$ cat /tmp/kj | xargs ~/ptII/adm/copyright/chkcopyright >& /tmp/kcj
bash-3.2$ grep 'blank' /tmp/kcj
./actors/src/org/sdm/spa/FileFetcher.java: saw only blank lines in copyright, expected 2
./actors/src/org/sdm/spa/FileStager.java: saw only blank lines in copyright, expected 2
./actors/src/org/sdm/spa/GridFTPUpdated.java: saw only 1 blank lines in copyright, expected 2
./actors/src/org/sdm/spa/ParameterizedGlobusJob.java: saw only 1 blank lines in copyright, expected 2
./actors/src/org/sdm/spa/RunJobGridClient.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/kar/KARAlreadyCachedException.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/kar/KAREntry.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/kar/KARFile.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/kar/KARManifest.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/moml/CompositeClassEntity.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/moml/PropertyAttribute.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/moml/PropertyEntity.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/objectmanager/cache/CacheException.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/objectmanager/InvalidMetadataException.java: saw only 1 blank lines in copyright, expected 2
./core/src/org/kepler/sms/SemanticType.java: saw only 1 blank lines in copyright, expected 2
./data-handling/src/org/kepler/dataproxy/datasource/DataSourceInterface.java: saw only 1 blank lines in copyright, expected 2
./ecogrid/src/org/ecoinformatics/seek/ecogrid/EcogridPreferencesTab.java: saw only 1 blank lines in copyright, expected 2
./ecogrid/src/org/ecoinformatics/seek/ecogrid/MetadataSpecificationInterface.java: saw only 1 blank lines in copyright, expected 2
./ecogrid/src/org/ecoinformatics/seek/ecogrid/quicksearch/DataSearchResultTree.java: saw only 1 blank lines in copyright, expected 2
./ecogrid/src/org/ecoinformatics/seek/ecogrid/SemRegIndex.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/component/OpenCompositeAction.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/kar/OpenArchiveAction.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/LibrarySearcher.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/LibrarySearchResultPaneFactory.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/LibrarySearchResults.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/PreferencesTabFactory.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/RemoveActorAction.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/SimpleLibrarySearcher.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/TabPaneFactory.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/TreeAction.java: saw only 1 blank lines in copyright, expected 2
./gui/src/org/kepler/gui/WelcomeScreen.java: saw only 1 blank lines in copyright, expected 2
./opendap/src/org/kepler/dataproxy/datasource/opendap/DapObjectsToToken.java: saw only blank lines in copyright, expected 2
./opendap/src/org/kepler/dataproxy/datasource/opendap/DapObjectsToType.java: saw only blank lines in copyright, expected 2
./opendap/src/org/kepler/dataproxy/datasource/opendap/OpendapDataSource.java: saw only blank lines in copyright, expected 2
./opendap/src/org/kepler/dataproxy/datasource/opendap/OpendapDataSourceODC.java: saw only blank lines in copyright, expected 2
./opendap/src/org/kepler/dataproxy/datasource/opendap/TokenMapper.java: saw only blank lines in copyright, expected 2
./opendap/src/org/kepler/dataproxy/datasource/opendap/TypeMapper.java: saw only blank lines in copyright, expected 2
./sms/src/org/ecoinformatics/seek/sms/AnnotationEngine.java: saw only 1 blank lines in copyright, expected 2
./sms/src/org/ecoinformatics/seek/sms/OntologyCatalog.java: saw only 1 blank lines in copyright, expected 2
bash-3.2$

Will do this as part of the release process.

All copyrights are now the same, except for files that had non-UC copyrights.

The sources in tests/src/ have old and inconsistent copyrights.

added a flag to update the copyrights for tests. all tests are now updated.

Original Bugzilla ID was 4373