[bz4647788] Don't make unnecessary calls to the shell for file system commands

[add0n]

The yuidoc script is bad about this.

[mridgway]

Are there other places that we need to clean up other than yuidoc? If not, this can be closed since #243 is merged.

[drewfish]

We spawn a java process to generate instrumented code for code coverage, in app/commands/test.js.

[mridgway]

Ok that makes sense. Once Arrow supports code coverage and is open sourced we will be able drop the java code.

[rwaldura]

we'll use Istanbul for code coverage