Bundle does not use platform baseDir

**I'm submitting a bug report**

* **Library Version:**
0.31.3

**Please tell us about your environment:**
* **Operating System:**
OSX 10.12.6

* **Node Version:**
7.2.1

* **NPM Version:**
4.1.1

* **Browser:**
all

* **Language:**
ESNext

* **Loader/bundler:**
SystemJS

**Current behavior:**
When defining the `platform.baseDir` property in config the `baseDir` value is not used.

* **What is the expected behavior?**
I expected that the cli would use the `baseDir` as the value to define the base directory in which to write the bundles and find the index file.
For example: if I define the `baseDir` as "wwwroot", the index as "index.html" and the output as "scripts" then I would expect the bundler to write the bundle (e.g. "vendor-bundle.js") to "wwwroot/scripts/vendor-bundle.js" and to update the script src in "wwwroot/index.html" to point to "scripts/vendor-bundle.js".

* **What is the motivation / use case for changing the behavior?**
For my use case I am using Aurelia served from an aspnet core project, which provides the rest api. I want to be able to keep the client source in a single child folder (named "Client" in my case) and have the cli spit out the bundles into the wwwroot folder.

I have a fix for this, and am happy to submit a PR, but I wanted to first confirm that this is a bug and that I'm not just misunderstanding the intended use case for the `baseDir` property.