coder_upgrade.function.inc: refactor #hook_permission to...

coder_upgrade.function.inc: refactor #hook_permission to hook_upgrade_hook_perm_alter(), refactor #descriptions_permissions to use the convert_return() pattern (use cases 1 and 2), refactor doc_comment checking in coder_upgrade_convert_update_N() to revert to that in hook_upgrade_hook_alter(); tests/samples directory: update the input and expected test file: example.module.