What's the difference between configuration files in the server/*/conf directory and in the files in the server/*/deploy directory?

Not only are there files in the deploy directory itself, but within the archive files within that directory.

This confuses me, as I'm not sure what the difference between putting them in any of these three locations: conf, deploy, EAR/WAR/JAR/SAR...

Examples of files include:
- jboss-service.xml
- login-config.xml
- jndi.properties
- AND MANY MORE

Somebody please help me sort out this confusion. Thanks!