Angular CLI finally supports HMR starting 1.0.0-beta.22. But to enable it needs app changes:https://github.com/angular/angular-cli/blob/master/CHANGELOG.md
NOTICE Hot Module Replacement (HMR) is enabled for the dev server.
The project will still live reload when HMR is enabled,
but to take advantage of HMR additional application code is required
(not included in an angular-cli project by default).
for information on working with HMR for Webpack.
Here’s a working example with these changes: https://github.com/jschwarty/angularcli-hmr-example