Made it a bit more extensible and reusable

[Kojotto]

Moved all the functions that are used inside the template to be available from the controller.

What you can do now is something like this:
.directive("treecontrolfoldering", function() {
return {
restrict: "A",
require: "treecontrolFoldering",
link: function(scope, element, attributes, ctrl) {

                var isolateScope = element.isolateScope();

                ctrl.ensureDefault(element.isolateScope().options, "nodeFolderType", "FolderType");

                isolateScope.folderTypeClass = function (node) {
                    var destinationType = scope.foldering.getDestinationObject(node);
                    return destinationType.cssClass;
                };

                ctrl.defaultIsLeaf = function(node) {
                    return (!node[isolateScope.options.nodeChildren] || node[isolateScope.options.nodeChildren].length === 0) &&
                        (!node[isolateScope.options.nodeFolderType] || node[isolateScope.options.nodeFolderType].length === 0);
                }

                isolateScope.options.isLeaf = ctrl.defaultIsLeaf;

                var orderBy = "| orderBy:'Name'";
                var orderByFolderType = "| orderBy:'toString()'";

                var template =
                    '<ul ' + ctrl.classIfDefined(isolateScope.options.injectClasses.ul, true) + '>' +
                        '<li ng-repeat="node in node.' + isolateScope.options.nodeFolderType + ' | filter:filterExpression:filterComparator ' + orderByFolderType + '" ' + ctrl.classIfDefined(isolateScope.options.injectClasses.li, true) + ' class="folder-type">' +
                        '<i class="type-icon" ng-class="folderTypeClass(node)"></i>' +
                        '<div class="tree-label ' + ctrl.classIfDefined(isolateScope.options.injectClasses.label, false) + '" tree-transclude></div>' +
                        '</li>' +
                        '<li ng-repeat="node in node.' + isolateScope.options.nodeChildren + ' | filter:filterExpression:filterComparator ' + orderBy + '" ng-class="headClass(node)" ' + ctrl.classIfDefined(isolateScope.options.injectClasses.li, true) + '>' +
                        '<i class="tree-branch-head" ng-class="iBranchClass()" ng-click="selectNodeHead(node)"></i>' +
                        '<i class="tree-leaf-head ' + ctrl.classIfDefined(isolateScope.options.injectClasses.iLeaf, false) + '"></i>' +
                        '<div class="tree-label ' + ctrl.classIfDefined(isolateScope.options.injectClasses.label, false) + '" ng-class="[selectedClass(), unselectableClass()]" ng-click="selectNodeLabel(node)" tree-transclude></div>' +
                        '<treeitem ng-if="nodeExpanded()"></treeitem>' +
                        '</li>' +
                        '</ul>';

                ctrl.template = ctrl.recompileTemplate(template);
            }
        }
    });