A new XML Security Tools build (I20090315175418) is available for download: http://build.eclipse.org/webtools/committers. This version contains a lot of changes and several bug fixes: Signature/ Encryption is now possible over selections or XPath expressions again (there has been a nasty bug which resulted into a WRONG_DOCUMENT_ERR). All quick functionality is working, including the support for the latest keystore extensions that have been added to XML Security Tools a little while ago.
And the integration into the rest of the Web Tools Platform was extended. XML Security is no longer a separate category in the preferences: it is now a child entry in the XML category. The same happened to the XML Signatures view, which is now a child entry in the XML category.