The configuration on server.conf is really tedious. Every time I upgrade my system I take 25 minutes instead of 2, this is because I have to stop the confluence instance again after upgrade and redo every custom configuration.
The most annoying thing a have to do (so annoying that I keep my instance out of date and wait some updates until the upgrade worthwhile) is:
1. Stop confluence. Again (this take time on my system)
2. Move (don't copy) activation-1.0.2.jar and mail-1.4.1.jar from <confluence-install>/confluence/WEB-INF/lib to <confluence-install>/lib.
(Are you seriously? Why a have to do that? And why the confluence package don't do that by default? Some freak bug like some microsoft products? Just kidding )
3. I'm smart so I don't type again the configuration on server.xml, I make a copy, but I cannot ensure that my copy just change the lines for mail config and I have to make a diff on the command line to be sure that I will not break the system and have to stop confluence again.

Not least but important too. I have to take care of the security of that file, if someone read that content my account is compromised. Well my system is secured and only root has access but who knows, and what about shared servers that others can be using, like universities?

Jira have a configuration for SMTP SSL email, and this is not broken between upgrades because is in the database.

This is easy to implement in spring config. So be nice with me and other sys devs.

By the way, I have other configurations like SSO with Crowd. Is tedius too, every config that depends on files and cannot be automatic created by confluence (and jira, and stash, and crowd) is tedius to maintain between upgrades.

Keep all on database and make the upgrade a easy, funny and routine part of your products