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This script will automatically set the glyph overlap bits for glyphs that have overlapping contours. Atm, it will only work on ufos since AFAIK .glyphs files do not have the ability to set these bits yet.
I originally wrote this as a ufo2ft filter. However, on David Berlow families, it was agonisingly slow. The pain was similar to installing win 95 using floppy disks.
I may be cheeky and throw this into the gftools builder for fonts that have less than 10 masters.