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:
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.)
View solution in original post
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.