Once again the angular team makes things harder for not real reason =(
I had this problem and after Googling around fruitlessly I wondered if they had changed relative paths somehow as well as renaming angular-cli.json.
A little further up in the file I found the line:
Yeah, just change:
"../node_modules/jquery/dist/jquery.js",
"../node_modules/tether/dist/js/tether.js",
"../node_modules/bootstrap/dist/js/bootstrap.js"
to
"./node_modules/jquery/dist/jquery.js",
"./node_modules/tether/dist/js/tether.js",
"./node_modules/bootstrap/dist/js/bootstrap.js"