Running mvn install will build/compile.
Inside pkg there's the steps necessary to create the agent-side package file. Then deploy just shows where the jar and the zip should be copied. You'll notice your agents go down for an ugprade and to get the server side workign you'll have to restart.
Add the following lines to /conf/teamcity-server-log4j.xml
Make these instructions obsolete with better configuration/scripts/etc...