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manifest.xml is used in the legacy rosbuild build system while package.xml is used in the catkin build system

In package.xml, you need to add the following lines:

<build_depend>nav_msgs</build_depend>
<build_depend>tf</build_depend>

<run_depend>nav_msgs</run_depend>
<run_depend>tf</run_depend>

In addition, you can find the complete code for this tutorial at this link:

https://github.com/ros-planning/navigation_tutorials/tree/indigo-devel/odometry_publisher_tutorial