Remove duplicate nginx_log_dir.
Remove munin passenger plugins.

The format of passenger-status and passenger-memory stats changed with Passenger 4.x. These plugins no longer work. I've never found these plugins to be that helpful because:

- We lock down the number of worker processes so it never changes. No sense in graphing it.
- The biggest memory load in the system by far is the passenger workers. It's just as easy to monitor system memory as a whole vs monitoring the passenger memory. What would be really useful is monitoring memory by worker, which this plugin doesn't do.