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In the navigate.launch file, this line points to a file called move_base.launch.xml I made a copy of the file and went through its contents.

<include file="$(find turtlebot_navigation)/launch/includes/move_base.launch.xml">
 ...
</include>

In that file there's a section that reads like this:

<remap from="cmd_vel" to="navigation_velocity_smoother/raw_cmd_vel"/>

I rewrote the line as this:

<remap from="/app_manager/application/cmd_vel" to="/app_manager/application/mobile_base/commands/velocity"/>

I then referenced the file from the navigate.launch file. This solved my problem.