It is the linear speed of the filament. However, in the firmware that ships with Cura for the Ultimaker-Original there is a bug that makes retraction slower then entered. Which is why 45mm/s is the default for the Ultimaker. After the fix a value of 20-25mm/s is more accurate.
Repetier lists mm/minute because that's what the firmware is actually reading. Cura uses mm/sec everywhere as those values are smaller and easier to comprehend in my book. mm/minute is a left-over from CNC milling which is much slower in movement then printing.
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aaron 2
Yes, retraction distance is the distance the filament is moved by the extruder gear in mm. However, this will not be exactly the case on the hot end. Filament will not necessarily move (for example) 4mm on the hot end side when the gears move it 4mm because of things like play in the bowden clamps and slight room in the bowden tube etc.
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