For example, does Splunk ignore server.conf, distsearch.conf, or any other conf files if they're located in an apps directory?
Also, are there any other cases where a particular conf file's location is restricted to a subset of the otherwise generally available set of conf directories, as listed in this topic:
http://www.splunk.com/base/Documentation/latest/Admin/Wheretofindtheconfigurationfiles
Those files should work even in an app directory. If they do not, please file a defect.
There are a few exceptions: conf.conf can't work in an app, but we don't really doc that as useful to users anyway (it isn't.)
Your configuration files may not be ignored -- it could be that there is another file (of the same name) that takes precedence. This topic is pretty well documented so I will refer you to our doc for further reading.
Those files should work even in an app directory. If they do not, please file a defect.
There are a few exceptions: conf.conf can't work in an app, but we don't really doc that as useful to users anyway (it isn't.)