Hi wipster
I understand your dissatisfaction concerning some documentations for ILIAS development and ILIAS plugin in particular. The ILIAS community is – compared to other open-source projects – quite small and tries with best effort to satisfy interests of different usergroups. We definitely want to improve the guidelines and documentations for developers. This is one topic of many the newly introduced Teachnical Board (http://www.ilias.de/docu/goto_docu_grp_5089.html ) is aware of. Unfortunately this will take some time...
Adressing your problem I try to understand the use case you want to implement. Repository-Object-Plugins are designed to act like other Objects/Tools in ILIAS and get their permissions through ILIAS RBAC. This means if you define the rule-sets like mentioned above, those permissions are aplied for newly created objects in your courses.
But if your intention is to override this and implement some own procedure of appllying permissions, you could habe a look at the GUI-class which delegated this functionsality through the ILIAS-Administration. Most of this is done in ilObjRoleGUI, e.g. the adaption of permissions from a template in method adoptPermSaveObject(). It uses the global $rbacadmin to 1. deleteRolePermission() and then 2. copyRoleTemplatePermissions()
I hope this gives you a hint how to implement your special feature. Maybe you could post a link to a git-repository with your plugin here so I could just have a look at it, maybe I can give some more hints.
Best regards
Fabian