Thanks for the information on making archives. I’ve created a current one (minus the world folders and the dynamap/web folder (that was 22GB!)) and posted it here for you to check out:
http://www.mediafire.com/file/93ui2cyfnjtk975/MCHills_Mods-Archive3.tar.gz
Regarding the console commands, what I’m looking for is a way to interact with the live server and players on it via a console/terminal window, like how you could from the line under the log files in WebUI. I don’t have anyone with OP status on our server, so when things come up that need fixed or whatever I would do it through there using the commands from the various plugins or minecraft server commands from here: http://minecraft.gamepedia.com/Commands#Summary_of_commands. Sorry if this is a basic question, I’m not terribly familiar with these things.