You can use whatever features you feel like in ioNinja, it's got a number of useful options. nxTools on the other hand is a bit trickier since I've included a number of it's features as built-in commands in ioFTPD over time. It's easy to spot which these are because under the command permission section of the .ini you'll already find entries for things like site who, open, and close. Just don't install those commands by leaving the TCL script definition out of the custom commands section and you'll be fine. After that just choose what you want from the config file. It's just a matter of preference at that point.
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