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Depending on what you intent to do I see two possibilities:

Call your C program/shell script from ROS, either by system() within a node or you can also rosrun/roslaunch non-ROS executables.
Integrate your code with ROS by building it as a ROS package, writing a ROS interface or making it available as a library.

Some hints might be here: http://www.ros.org/wiki/UsingThirdPartyLibraries

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