In the sentence,
Django encourages beautiful URL design and doesn’t put any cruft in URLs, like .php or .asp.
Badly designed, unnecessarily complicated, or unwanted code or software. cruft | Definition of cruft in English by Oxford Dictionaries
Origin 1950s (in the sense ‘rubbish, detritus’): origin unknown.
It's easy to understand whereas difficult to memorize its spelling.
It has no shared parts with its synonyms 'rubbish' and 'detritus'.
Compared with 'craft' to associating it, seems make no sense.