Cheffile and Vagrantfile updates, especially setting specific cookbook versions

 - To avoid unexpected issues a consistent set of cookbook versions is being used.
    -- the mysql cookbook is 'derated' from the current 5.1.0 to 4.1.2 because in the 5.x series a bunch of additional configuration is needed. Updating to 5.1.x permits newer cookbooks elsewhere as well.

 - The AMI id used for AWS is updated to a standard version of Ubuntu 12.04 that includes the openssl fixes from 8th April. This version, like the last, uses temporary file storage, not EBS

 - I have removed the explicit use of elifesciences php cookbook because the bug referenced (https://github.com/opscode-cookbooks/php/pull/54) has been committed to mainstream.

 - The JSON block includes a setting for the 'apt' cookbook so that it will check for updates no sooner than 10 minutes, not 24 hours, to workaround an issue with important updates.

 - I have added a gitignore file for the common additional files.

I have tested this file on two AWS builds and it all seems good!

Note
====
There is a message output at the start of the run, containing:

    ''SSL validation of HTTPS requests is disabled. HTTPS connections are still
encrypted, but chef is not able to detect forged replies or man in the middle
attacks.''

I presume this is a new thing added to cookbooks recently. While it should probably be looked into it doesn't stop the build working and shouldn't affect our work.