Add warnings in site status page (end elsewhere?) to remove contrib module folders if added to core.

[klonos]

After #87 and #480, we might run into more cases where people upgrade Backdrop to newer versions that have included contrib modules in core but leave the respective old contrib module folders in their /modules directory. Now, we already have tried to make sure that these left-over modules are not called, but we can never be really sure of what issues might be caused by leaving duplicate modules both in core and contrib module directories. Can we put some message/warning in place that "nags" people telling them that it is safe and recommended to remove the module folders from /module directory?

[klonos]

...I just noticed that there is warning in the modules page. That's great, but I feel that there should be a warning in the status page too as well as a message shown in every /admin page (like the critical updates warnings).

[quicksketch]

Now, we already have tried to make sure that these left-over modules are not called, but we can never be really sure of what issues might be caused by leaving duplicate modules both in core and contrib module directories.

Some of the problems we were having was because we couldn't get to the update.php script. As part of the updates to move pathauto and token into core, we delete the entries from the "system" table, effectively disabling them. Then making it so you can then no longer turn them back on, these old modules are no more dangerous than having an unported Drupal 7 module in your modules directory, which if it ran any code, may also cause some serious problems on your site.