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ARC file: This is a wavelength calibration image. Our default is to use a NeNeAr combination, which has produced stable wavelength solutions. An arc line identification plot for this lamp combination may be found here; associated references for the line lists are here.
BLUE and RED flats: As in many spectrographs which cover a large wavelength range, it is difficult to obtain a single flat field exposure the covers the full spectral range at adequate signal-to-noise ratio without saturating. To work around this problem the pipeline takes in pairs of flats which we denote as "blue" and "red." These are obtained using different voltage settings on the variable quartz lamp in the Baade dome.
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Once your file names are entered in, you will probably want to set preferences for the reduction stages. To do this, select the "Options->Preferences" pane from the menu bar. This will realize the following window: 