There are 4 main places in which Cocoon is configured:
sitemap.xmap -- the Sitemap. By default, located in $CATALINA_HOME/webapps/cocoon directory.
cocoon.xconf -- configuration file containing Logicsheet registrations. Specifies, sitemap.xmap location and other such parameters. By default, located in $CATALINA_HOME/webapps/cocoon/WEB-INF directory.
web.xml -- servlet deployment descriptor. Specifies location of cocoon.xconf, log file location, caching configuration, and other such parameters. Located in $CATALINA_HOME/webapps/cocoon/WEB-INF directory.
cocoon.roles -- mapping file for core Cocoon component names and implementation classes. For example, if you want to use a parser other than the default one, you need to modify this file.
Logging level is set in the web.xml file.
Java files (including sitemap_xmap.java) are stored in $CATALINA_HOME/webapps/work/localhost_8080%2Fcocoon/org/apache/cocoon/www
Caching in Cocoon is configured using Avalon components defined in cocoon.xconf