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Application-level permissions are implemented as OAuth Scopes and captured in OEP-4. This is not what you guys are currently asking about.
System-wide Roles are a set of roles that are to be used across the platform. They are configurable for the instance of the platform. That is, different Open edX instances may have different sets of Roles.
System-wide User-Roles are mappings between users and system-wide roles, stored in a centralized user service (LMS today). They are communicated in *JWT Tokens* so  so different IDAs can enforce them.
IDA-specific Roles are mappings between System-wide Roles and IDA-specific Roles. These are specific to the IDA and configurable for the instance of the platform.
IDA-specific Role-Permissions are mappings between IDA-specific Roles and IDA-specific Permissions.
IDA-specific Permissions are relevant to the features specific to the IDA and implemented as described in OEP-9.

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