Nick's first question is whether this is a problem, and in storing sources, if it is handy to have a glyph composited, remaining linked to the source glyph, including transformation by whatever useful means the design tool will allow, then do it. For font generation, I'd decompose and correct path directions on anything other than x and y positioned composite glyphs.
When creating auto hinted CFF fonts in FontLab – particularly when using Adobe’s Auto-Hint script, I have found you get better results if everything is decomposed first. I think this may be due to subroutine building and hint replacement.
If one is autohinting, it doesn't matter much when the decompositing happens, I think. Also, I'm pretty sure cff has nested subroutines so, I don't think you save by decompositing everything. But I'd like to know if cff subroutines use mirroring and flipping matching to compress, or whether the orientation of subroutined curve segment must match...
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Why decompose? Isn’t the idea to reduce file size?
Sometimes they end up having inverse contour direction.
Use them at the beginning of the design process. Once you are happy, decompose and correct path direction.
Also, I'm pretty sure cff has nested subroutines so, I don't think you save by decompositing everything. But I'd like to know if cff subroutines use mirroring and flipping matching to compress, or whether the orientation of subroutined curve segment must match...