Merge pull request #3 from muffinresearch/modify-config-path-for-docker

Modify config path in index.js
pull paths from config
move npm/bower bump into Makefile (bug 1094266)
v1.0.91 allow-root for bower
v1.0.92 simplify code related to docker now that gulp doesn't handle bower/npm bump
use r.js proper rather than amd-optimize (bug 1092718, 1078093)