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There is this amazing new thing called "search the forums", you write in what you want to know and it magically gives you a list of topics that will likely answer any question you may have. I predict it's going to be quite revolutionary, you should try it out!
A Combat Routine or CR for short, is much like a plugin in regards to how it works with the Honorbuddy client. Depending on the CR it may do everything or only a few things but, at it's essence a CR will do the DPS or Healing rotation for your class. Take a look at the CR section of the forums and read a few...
The combat routine does one and only one thing, as the name implies, combat. During any time your character is in combat/aggro-ed, the "botbase/profile" will relinquish control of the character to the combat routine. The combat routine will maintain control until the character is no longer aggro-ed or in combat, at which point it will return control to the botbase/profile. The one exception to this, that I can think of off the top of my head, is DungeonBuddy, which scripts the combat allowing the combat routine to work in conjunction with the script.