Prevent removing permissions of disabled modules

Issue Summary

When "Disable developer modules" is triggered, developer modules are disabled. Visiting and submitting the permissions form on admin/user/permissions will thereby remove all permissions of disabled developer modules.

Actually, this is a Drupal core bug. Only not installed/uninstalled modules should be left out in the permissions form. Disabled modules can be re-enabled at any time.

So we have 4 options to fix this:

1) Output a message on top of the form to allow the user to re-enable the disabled developer modules, so they do not lose any data.

2) Use hook_init() to re-enable any disabled developer modules on that page, and hook_form_alter() to add a submit handler to the form to disable them again. (Will fail when user only visits the page, but does not submit the form.)

3) Use hook_form_alter() to add all disabled developer modules to the form.

4) Move this issue to Drupal core and fix the underlying bug there.