Bug 126779 [IDE] Removed deprecated project capabilities API and implementation
It was created then deprecated before 2.0 shipped. As has never been API and we don't use it we should delete it.
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/internal/ide/dialogs/RemoveCapabilityWizard.java
/**
     * Update the project natures
     */
    private boolean updateNatures() {
        
        WorkspaceModifyOperation op = new WorkspaceModifyOperation() {
            protected void execute(IProgressMonitor monitor)
                    throws CoreException {
                try {
                    IProjectDescription description = project.getDescription();
                    String[] oldIds = description.getNatureIds();
                    ArrayList newIds = new ArrayList(oldIds.length);
                    for (int i = 0; i < oldIds.length; i++) {
                        boolean keepNature = true;
                        for (int j = 0; j < natureIds.length; j++) {
                            if (natureIds[j].equals(oldIds[i])) {
                                keepNature = false;
                                break;
                            }
                        }
                        if (keepNature)
                            newIds.add(oldIds[i]);
                    }
                    String[] results = new String[newIds.size()];
                    newIds.toArray(results);
                    description.setNatureIds(results);
                    project.setDescription(description, monitor);
                } finally {
                    monitor.done();
                }