Please provide us with the following information:

OS?

Windows 7, 8 or 10. Linux (which distribution). Mac OSX (Yosemite? El Capitan?)
Windows 10

Versions.

Please run ng --version. If there's nothing outputted, please run in a Terminal: node --version and paste the result here:
Beta 20

Repro steps.

Was this an app that wasn't created using the CLI? What change did you do on your code? etc.
Changed angular-cli.json root folder, prefix,StyleExt

The log given by the failure.

Normally this include a stack trace and some more information.

Mention any other details that might be useful.

When updating to new version of angular-cli, it ignores custom root and prefix defined in angular-CLI.json

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Thanks! We'll be in touch soon.