Is there a way to apply clean up paths and correct path directions at export?

I’m exporting a variable font and would like to decmpose some component glyphs at export, for some reason one of my glyphs isn’t being decomposed to something interpolable, if I manually decompose and remove overlaps and correct path directions, it becomes interpolable, is there a way to apply those steps as a filter?

Those steps you took manually will produce incompatible outlines in most cases.
You can experiment with the “reverse” setting of the component that might need it.

Can you explain your setup in more detail?

I sent the file, its specifically for the roman numeral glyphs, for example for IV:

I and V are components, the top and bottom bars are paths.

How do you use the reverse setting?

I’d first try making the bars components as well. Don’t know if that will solve the issue, but the developers have long discouraged combining components and paths in the same glyph.

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the remove overlap filter that is run on export is producing different staring points in the different masters. I don’t know why, yet. You don’t need to remove the overlap. Or do you have a reason to do so?

The reason why we remove overlap is because users sometimes outline our fonts, and if the overlaps are in there then that just looks like a mistake. The other issue is sometimes you get rendering issues like such:

See where the components and paths edges overlap:

Now we could edit the components so that edges don’t overlap but you’d still have the former issue.

Well, easiest way out is to squish them a tiny little bit. Move the components up three units and scale them (vertically) down by six.