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I have released two font production scripts under the GPL. Both can be downloaded from Dunwichtype.com.
DTF Decomposer is a script intended for producing final versions of fonts that contain overlaps and composites that would otherwise require manual intervention. It first decomposes glyphs supplied in a list. It then removes overlaps in all glyphs and corrects path directions.
DTF Mark overlaps checks all glyphs for overlaps and marks a glyph when an overlap is found. It can find overlaps in glyphs that contain only outlines, only components, or outlines and components. It is not especially fast, but it is much faster than manual inspections. Sometimes glyphs that do not actually contain overlaps will be marked. This is because Fontlab's remove overlap function removes stray anchor points it deems unnecessary, such as anchor points on straight lines.
Neither script has been optimized to run as fast as it could, but they are both a lot faster than manual operations, especially when finishing families.