It appears as if the plugin (or one of its dependencies) is not correctly packaged for npm. After adding the plugin to the config file like this:
23:33:42.559 2016-01-11 Monday
23:34:06.808 [pimatic] Starting pimatic version 0.8.98
23:34:13.721 [pimatic] Loading plugin: "pimatic-cron" (0.8.5)
23:34:15.931 [pimatic] Loading plugin: "pimatic-mobile-frontend" (0.8.81)
23:34:21.150 [pimatic] Installing: "pimatic-johnny-five" from npm-registry.
23:34:29.313 [pimatic, npm] http GET https://registry.npmjs.org/pimatic-johnny-five
23:34:32.304 [pimatic, npm] http GET https://github.com/mwittig/etherport.git
23:34:32.609 [pimatic, npm] http GET https://registry.npmjs.org/particle-io
23:34:32.709 [pimatic, npm] http GET https://registry.npmjs.org/raspi-io
23:34:32.799 [pimatic, npm] http GET https://registry.npmjs.org/firmata
23:34:33.678 [pimatic, npm] http GET https://registry.npmjs.org/johnny-five
23:34:33.769 [pimatic, npm] http GET https://registry.npmjs.org/oled-font-5x7
23:34:33.859 [pimatic, npm] http GET https://registry.npmjs.org/oled-js
23:34:33.906 [pimatic, npm] http GET https://registry.npmjs.org/pimatic-plugin-commons
23:34:37.384 [pimatic, npm] http 200 https://github.com/mwittig/etherport.git
23:34:37.663 [pimatic, npm] ERR! not a package /home/pi/pimatic-app/tmp/npm-1787-omwKUTnO/1452555272054-0.5591643648222089/tmp.tgz
23:34:37.878 [pimatic, npm] ERR! Error: ENOENT, open '/home/pi/pimatic-app/tmp/npm-1787-omwKUTnO/1452555272054-0.5591643648222089/package/package.json'
23:34:37.911 [pimatic, npm] ERR! If you need help, you may report this *entire* log,
23:34:37.921 [pimatic, npm] ERR! including the npm and node versions, at:
23:34:37.941 [pimatic, npm] ERR! <http://github.com/isaacs/npm/issues>
23:34:37.964 [pimatic, npm] ERR! System Linux 4.1.13+
23:34:37.988 [pimatic, npm] ERR! command "/usr/local/bin/node" "/usr/local/bin/npm" "install" "pimatic-johnny-five"
23:34:38.001 [pimatic, npm] ERR! cwd /home/pi/pimatic-app
23:34:38.085 [pimatic, npm] ERR! node -v v0.10.24
23:34:38.094 [pimatic, npm] ERR! npm -v 1.3.21
23:34:38.113 [pimatic, npm] ERR! path /home/pi/pimatic-app/tmp/npm-1787-omwKUTnO/1452555272054-0.5591643648222089/package/package.json
23:34:38.131 [pimatic, npm] ERR! code ENOENT
23:34:38.149 [pimatic, npm] ERR! errno 34
23:34:38.237 [pimatic, npm] ERR!
23:34:38.246 [pimatic, npm] ERR! Additional logging details can be found in:
23:34:38.255 [pimatic, npm] ERR! /home/pi/pimatic-app/npm-debug.log
23:34:38.264 [pimatic, npm] ERR! not ok code 0
23:34:38.384 [pimatic] Error running "npm install pimatic-johnny-five"
23:34:38.442 [pimatic-cron] the time is: Mon Jan 11 2016 23:34:38 GMT+0000 (UTC)
23:34:39.334 [pimatic-mobile-frontend] packing static assets
23:34:41.407 [pimatic-mobile-frontend] packing static assets finished
23:34:41.449 [pimatic-mobile-frontend] rendering html
23:35:04.192 [pimatic-mobile-frontend] rendering html finished
23:35:04.337 [pimatic] Listening for HTTP-request on port 80...
https://github.com/mwittig/etherport