You're trying to be that organized, eh?
Well, if you comment out all the .cfg files in Nagios.cfg, nagios will assume that those files don't exist, because they're not being checked when Nagios starts. So you have no hosts, no services, no host groups, no contacts...well, you get the idea.
What did you set your prefix to when you configured Nagios for the install? That's not the default path for the $USER1$ macro; it's /usr/local/nagios/libexec.
I don't really see the point to having all these different directories, though. If it's something you really want to do...I suppose you could create a bunch of small .cfg files...like, say you have 3 hosts, you create 3 hosts.cfg files: one in each directory for your hosts, and then just add those entries to nagios.cfg in your central nagios/etc/ subdirectory. I have no idea if that will work, but it's worth a shot.
Of course, there will be .cfg files for which that won't make any sense to make different versions in different directories, such as resource.cfg, hostgroups.cfg, servicegroups.cfg, misccommands.cfg, off the top of my head.
Edited Tue Jan 10 2006, 10:11PM ]