Unfortunately I've find a lot of places in JBossTools where InputStream & OutputStream are used and are not closed. Just make a search and inspect all over the code.
Here just list of places for org.jboss.tools.jsf plugin:
1) JSF2ComponentModelManager -> public static IDOMDocument getReadableDOMDocument(JarEntryFile file)
2) JSF2Util -> public static String readManifest(IProject project, String jarName) throws CoreException, IOException
3) JSF2TemplateManager -> public InputStream createStreamFromTemplate(String templateName)
4) JSF2ComponentsValidator -> protected boolean isValidate(IFile file)
5) XHTMLEntityResolver -> public static XMLInputSource _internalResolveEntity(... -> is.setByteStream(new LazyURLInputStream(physical));
6) XHTMLValidator -> stream = new FilteredInputStream(connect.getInputStream());