User configuration and atlassian configuration should be separate

Configuration items that need to be configured by the administrator are mixed with configuration items that are not meant to be end user configurable.

The biggest pain point here is bin/setenv.sh (which should be split in two and put in the conf directory as it's actually a configuration file) as STASH_HOME and JVM_XXX_MEMORY need to be set to run.

Everything above "In general don't make changes below here" should be in a separate file so that we can create templates for our configuration management systems (such as Puppet) and not have to update the template every time we upgrade Stash due to changes by Atlassian.