This is basically a “docs bug” report: Nova’s docs do not (anywhere that I could find!) specify this, but the main script must live in the foo.novaextension/Scripts directory. The relative path specified for the main key is relative to that subdirectory. The existing docs make no mention of this. Instead, they simply specify the existence of the main key and the conventional main.js, and note that the main key should point to the relative path for the script file. Presumably the boilerplate gets it right, but if you happen to have built up an extension without running the relevant boilerplate… well, I spent way too long banging my head against this. 
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