Upgrade should only enable PHP module if necessary

On test upgrades, I found out that the upgrade process pushes the PHP filter module and the PHP input format on me. Given that the primary reason to move this to a separate module is to serve security, IMHO we should not push this input format on sites (like my use case) where the PHP input format simply should not be there.

The offending update is in system_update_6009() and has a few problems:

- unconditionally removes the second input format, regardless of what it might be (although users are allowed to remove filters, rename formats, so format #2 might not be a PHP input format on a particular site) => leads to data loss
- unconditionally enables the PHP filter module
- unconditionally adds a new input format with this filter enabled

IMHO all these are wrong.

What we should do is to identify whether there was any input format which used the PHP filter, and only enable the module if there was at least one. I am not convinced we would need to overwrite any of the existing PHP input format's information (as mentioned above the code removed the old format and added a brand new one). As far as I see, the only thing we need to do is to enable the PHP filter module if required and update the input formats affected to point to the new evaluator. Although the code lives elsewhere, behavior was not changed, so caches should not be flushed, etc.

Unless there is a reason uncovered to add this as a completely new format, I think we can go with this solution. This keeps people who chose not to enable the PHP format in Drupal 5 and before without this format.

Issue where this update code was added for reference: http://drupal.org/node/46941