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It doesn't have to do with literate programming per se.

It has to do with a very widespread and powerful legacy system (with extreme requirements for backwards-compatability and portability) that happened to be written decades ago in, basically, Pascal.

Furthermore, the people doing this port don't seem to have total command of the tex infrastructure. This has held them back.

For instance, they didn't know what kpathsea was until well after they started their port ("As best we could tell kpathsea is a library to find fonts and scripts in the sprawling TeX distribution...", from http://texpadapp.com/2011/12/10/price-of-amessy-latex-not-fo...).

kpathsea is a basic library that anyone who has tweaked TeX configurations would know about. It has a certain syntax for subdirectory searching that you have to learn, as well as a utility command (kpsewhich) that you run quite a lot to debug "file-not-found" problems.

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