You can find empty text nodes using XPath, then remove them programmatically like so:
XPathFactory xpathFactory = XPathFactory.newInstance();
// XPath to find empty text nodes.
XPathExpression xpathExp = xpathFactory.newXPath().compile(
"//text()[normalize-space(.) = '']");
NodeList emptyTextNodes = (NodeList)
xpathExp.evaluate(doc, XPathConstants.NODESET);
// Remove each empty text node from document.
for (int i = 0; i < emptyTextNodes.getLength(); i++) {
Node emptyTextNode = emptyTextNodes.item(i);
emptyTextNode.getParentNode().removeChild(emptyTextNode);
}
This approach might be useful if you want more control over node removal than is easily achieved with an XSL template.