Periodically or when the application is reloaded, tomcat6 is logging this into catalina.out:
06-Jul-2012 17:30:07 org.apache.catalina.startup.HostConfig deployDescriptor
SEVERE: Error deploying configuration descriptor home.xml
server.xml:
<Host name="www.mysitecom" appBase="/home/myuser/webapps" autoDeploy="true">
<Alias>mysitecom</Alias>
<Context path="/manager" privileged="true" docBase="/home/myuser/manager"/>
<Context path="" docBase="/home/myuser/public_html" reloadable="true" cachingAllowed="false"/>
</Host>
Caching is disabled as this is still under heavy development; it's caused headaches. I've tried setting the logging to FINE, but, apart from giving me unrelated data, it's not provided anything helpful. The only two lines shown in catalina.out are those above.
The website appears to work normally, but this error is worrying.
It was caused by the default catalina automatic definition, left over from an earlier build. Moving the "/etc/tomcat6/Catalina/localhost" directory out of the Catalina folder worked. David's comment helped.