同じ手順を Windows 上の Git Bash にて行ってみた

$ git clone https://github.com/jsdoc3/jsdoc
Cloning into 'jsdoc'...
remote: Counting objects: 16429, done.
remote: Total 16429 (delta 0), reused 0 (delta 0), pack-reused 16429
Receiving objects: 100% (16429/16429), 16.16 MiB | 1.17 MiB/s, done.
Resolving deltas: 100% (8177/8177), done.
Checking connectivity... done.
Checking out files: 100% (620/620), done.

$ cd jsdoc/
$ ./jsdoc -T
js: exception from uncaught JavaScript throw: Error: Module "c:/Users/xxxxxx/Documents/GitHub/jsdoc/jsdoc.js" not found.

うわーん