Where should I put configuration files?

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Usually what works well is providing the file URI as a ROS parameter that you can set via the rosrun command line or in a launch file. You can pair this with putting the actual files in a foo_bringup or foo_config package, which contains the config (and launch) files. In the launch files you can then use the <param name='config_folder' value='$(find_package foo_bringup)/config' /> syntax.

There was a question a while back about downloading additional files for a package (and then finding these from within a node), which might contain useful information for you: http://answers.ros.org/question/10976...