This section contains general In-link settings, which are not related to links. In the current version, it has only one setting. ‘Select Module Root Category' allows the administrator to specify the module root category of In-link. Clicking on the folder shortcut button will pop up a category picker. 
The module root category is used in several ways. On the front-end, in the Default theme, the top menu links each module to its module root category. Therefore, the ‘Directory' menu item will open this category and its contents. In the Administrative Console, this setting provides a faster way to navigate in the module, as it presets the category for module-specific actions. 
Logically, the module root category defines the portion of the catalog tree that is designated only for the In-link categories. If you are using the categories to store items from multiple modules, this setting is not applicable to your situation.