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Each directory contains the design source and binary (.stl .hex etc) needed to construct each part of the turbidostat.
All directories (where applicable) contain a source/ directory. This directory contains the original design files for that component. If you are not making a derivative design you may safely ignore these directories.
led_board/ and mainboard/ contain subdirectories called production_files. These directories should be zipped as is and sent to PCB manufacturers.