Missing files are symbolic links, and unfortunately npm does not support symbolic links. As a workaround, you can replace links with your goals (and remove goals to prevent duplication).
eg. for the FFF frame with the structure:
./FFF -> Versions/Current/FFF ./Headers -> Versions/Current/Headers ./Versions ./Versions/A ./Versions/A/FFF ./Versions/A/Headers ./Versions/Current -> A
you can run the following (in bash) from the framework directory:
framework=FFF && rm $framework Headers && mv Versions/A/{$framework,Headers} . && rm -rf Versions
to change the structure to:
./FFF ./Headers
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