Read the agent install docs here (specifically the second yellow box in this section that mentions that message you posted):
I checked the agent log and there were several 'permission denied' messages so I ran the agent setup as root and it installed correctly with plugins, however, I have a sinking feeling that I should not have to execute setup as root. I will read the doc you linked now. Also, new problem, autodiscovery worked but shows tomcat down and apache down. I will check the jopr log.
You do not necessarily have to run the agent as root. It all depends on how much and how deep you want to manage your resources.
For example, there is a Postgres plugin that lets the agent probe the Postgres configuration file postgres.conf. However, by default, Postgres installs itself with very strict file permissions on that file - and if you run the agent as a non-root, non-postgres- privileged user, it won't be able to read that file and manage it (and you'll see agent log messages saying so).
The same is true for lots of other plugins that try to manage things that touch privileged files (like iptables and things like that; even JBossAS app servers might be installed with strict file privileges that might cause this).
If you run the agent as root, you are giving the agent privileges to manage all those things - if you don't, you are giving the agent restricted views of your managed resources. This might be what you want, hence, you don't have to run the agent as root. But if you don't run the agent as root, you must be willing to accept that the agent will not be able to manage some things and will log messages saying so.
Thanks again John! I chmoded the entire agen folder recursively 777 and was able to start and finish the agent install as my non-root user. Chod 777 is probably overkill I suspect. Will check out log to determine why running the agent as root failed to start tomcat or apache.