Bug Report or Feature Request (mark with an x)

- [x ] bug report -> please search issues before submitting
- [ ] feature request

Versions.

angular-cli: 1.0.0-beta.26
node: 7.4.0
os: win32 x64
@angular/common: 2.4.10
@angular/compiler: 2.4.10
@angular/core: 2.4.10
@angular/forms: 2.4.10
@angular/http: 2.4.10
@angular/platform-browser: 2.4.10
@angular/platform-browser-dynamic: 2.4.10
@angular/router: 3.4.10
@angular/compiler-cli: 2.4.10

Repro steps.

This is not a major bug but rather something thats slighly off skew

When I run
ng set defaults.styleExt scss

I expected only one change in the angular-cli.json : in the styleExt key value but git was reporting two changes

The log given by the failure.

Desired functionality.

No new line in the empty array value of the scripts key

Mention any other details that might be useful.