Change nginx.conf to only include .conf files

I'm doing this in a terrible way at the moment because I'm not being thorough and fixing the things this breaks - but I'd like to change this to include only *.conf files in the Nginx directories.  This is specifically to avoid /etc/nginx/custom-sites/local-nginx-example.conf-sample from being loaded in Nginx.  However, it also breaks the "default" files - which I'd recommend changing to default.conf instead.  The benefit of this is you can quickly backup a conf file by copying it to conf.bak and it won't get pulled in to Nginx.  I can be more thorough about this later.
Align all upload size limits at 50M

We had multiple upload limits in place in the nginx and PHP config files. This changes them all to 50M, which should be high enough for most local development.
Handle package status in provision.sh for repeat provisions

This treats provision.sh more like the provisioning script it should be and checks for the status of each package before adding it to the array of apt packages to be installed. If the array is not empty, `apt-get update` runs and then the `apt-get install` immediately after.

Sets us up to remove the initial provision flag, which was an ugly hack. Better yet, if a package fails to install the first time round, a quick `vagrant provision` should take care of it.
Move the MySQL configs down to the package installation check

Only sets these config parameters when needed
Comments clarification
Remove the initial provisioning flag that prevented repeat provisioning runs

Allows our individual package checking to do its work.

Need to correct the appending of our custom apt sources list as this makes the sources.list file grow and grow until the next `vagrant destroy`
Check for Composer in the right place
Provide our own default apt sources.list to append our custom sources to

The previous append method was adding our custom sources to the default sources.list every time that `vagrant provision` was run, causing many duplicate entries. Rather than deal with the logic of checking for existing lines in that file, we'll just take control of the entire thing by providing the default sources from Ubuntu 12.04 ourselves. There may be a better long term fix for this.
Calculate provisioning time in provision.sh
Move mockery to stable 0.8.0, at least temporarily
No need to update Composer on every provisioning
Refactor handling of Composer to be version based

More in line with how a provisioning script should handle things. If the expected version of Composer is not installed, either install it or update to that version. If the expected version is installed, don't waste time looking for the update.
Check for status of various vvv-phpunit dependencies before installing

Ideally we would check for version numbers as well, but the bash output just wasn't cooperating. I know this somewhat defeats the purpose of having dependencies managed by Composer itself, but it's sooooo slooooow waiting for it to hunt down updates. I'd rather tell it to only update when a version number does not yet exist.
General cleanup of provisioning comments
No great reason to show all network interfaces at the end of provisioning. Something smarter should take care of this.
Formatting tweaks to output of scripts during provisioning
We have no reason to check the conf.d or sites-enabled directories with our setup for nginx
Remove worker_cpu_affinity directive

worker_cpu_affinity was already commented out and served no purpose as this was the default setting for the 4 worker_processes that we have set. This is a really interesting setting for anyone that wants to know more - http://www.kutukupret.com/2010/11/18/nginx-worker_cpu_affinity/
Tweak some of the WP specific nginx documentation
Improve nginx site example configuration