implementation of permissions - default permission at the application management panel?

IN the permission definition did you define all the role defaults for all group types?

I believe so... at the group level.. all the right permissions are set by default as expected.. let me know if you need more, but the permissions implementation looks similar to below:

 permissionController.Register(
              new MapAppPermission(
                CreateMapApps,
                _translation.GetLanguageResourceValue("Permission_MapApp_CreateMapApps_Name"),
                _translation.GetLanguageResourceValue("Permission_MapApp_CreateMapApps_Description"),
                Applications.MapAppType._applicationTypeId,  
                new PermissionConfiguration()
                {
                    Joinless = new JoinlessGroupPermissionConfiguration { Administrators = true, Moderators = false, RegisteredUsers = false, Owners = true, Everyone = false },
                    PublicOpen = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false, Everyone = false },
                    PublicClosed = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false, Everyone = false },
                    PrivateListed = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false },
                    PrivateUnlisted = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false }
                }
              )
            );

I believe so... at the group level.. all the right permissions are set by default as expected.. let me know if you need more, but the permissions implementation looks similar to below:

 permissionController.Register(
              new MapAppPermission(
                CreateMapApps,
                _translation.GetLanguageResourceValue("Permission_MapApp_CreateMapApps_Name"),
                _translation.GetLanguageResourceValue("Permission_MapApp_CreateMapApps_Description"),
                Applications.MapAppType._applicationTypeId,  
                new PermissionConfiguration()
                {
                    Joinless = new JoinlessGroupPermissionConfiguration { Administrators = true, Moderators = false, RegisteredUsers = false, Owners = true, Everyone = false },
                    PublicOpen = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false, Everyone = false },
                    PublicClosed = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false, Everyone = false },
                    PrivateListed = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false },
                    PrivateUnlisted = new MembershipGroupPermissionConfiguration { Owners = true, Managers = false, Members = false }
                }
              )
            );

oh... wait.. all the roles.. so Owners, Managers, all of them? there are many...yes?

Can you verify that you are registering the Id of the new App?  To do this, your class that implements IPermissionRegistrar needs to exposes the IPermissionController or a method that can access the controller to your Create process.   The process needs to invoke IPermissionController.RegisterSecurableApplication(...)

No this is right...see new reply 

I think that is what I am missing (IPermissionController.RegisterSecurableApplication)... but I don't see it...

it looks like it's the IPermissionRegistrarController that I need to implement? is that right, it has the RegisterSecurableApplication.. 

No, the class you are defining them in already has it, you are using it to register the permissions (see your example)

However when you create an application you need to call it but its hidden in that plugin, so you need to expose that method somehow publicly, get the plugin and call it after your application is created

So.. if this is right.. for 9.x now I am looking for an example on how to implement this

 public void Register(IPermission permission)
        {
            throw new NotImplementedException();
        }

        public void RegisterSecurableApplication(Guid applicationId, Guid applicationTypeId, Guid containerId)
        {
            throw new NotImplementedException();
        }

This is an example method to add to your current permissionregistrar plugin

public  void RegisterApplicationSecurableId(Guid applicationId, Guid containerId)
{
	permissionController.RegisterSecurableApplication(applicationId, [Yoor Application Type Id], containerId);
}

Then your create process needs to call

PluginManager.Get<YourRegistrarType>().FirstOrDefault().RegisterApplicationSecurableId(applicationId,containerId);

OH!! okay... I didn't realize the RegisterSecurable  was right infront of me,

I'll work on this for a bit.. for the plugin manager, "AfterInitialization" event should do it? 

No you aren't doing this in an event.  Every time you create an instance of your application, it needs to be registered in the security system.  So somewhere you have logic I assume that creates the application in the group and you get the applicationId, thats where you need to get the plugin instance and call it