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What I don't know is which files to run as start-up(tele-op and autunomous, or just tele-op or just autonomous), or where to write the autonomous code.
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Sorry I wasn't clearer. None of the above. The Build Specifications folder under the cRIO will already contain a Deployment. That is the file that defines which files to download and to run. Clicking on the other files is still running source files.
Greg McKaskle