Issue title: Separate directories for map files
 Issue body: Hi!
I find it rather odd that the option mapRoot exists without a corresponding option which outputs the map files to said directory. I have to manually move them after transpiling, which is annoying.

Here is a SO question which is valid for my case aswell: https://stackoverflow.com/questions/43052200/can-i-place-webpack-source-maps-and-source-code-files-in-seprate-folders

I guess it's kinda related to: https://github.com/microsoft/TypeScript/issues/6723
 Comments: 
 Comment 0: Why did you ignore the issue template?

TypeScript [design non-goal](https://github.com/Microsoft/TypeScript/wiki/TypeScript-Design-Goals#non-goals):

> 4. Provide an end-to-end build pipeline. Instead, make the system extensible so that external tools can use the compiler for more complex build workflows.

 Comment 1: @kitsonk I don't really think this falls under `Provide an end-to-end build pipeline.`. The compiler produces 3 types of file as output, .js files, .js.map files, and d.ts files. You can currently control the output directory for two of those (`--outDir` and `--declarationDir`), why not the third ? Especially since we do have the option to set the `mapRoot` directory.
 Comment 2: Not much different from `declarationDir` but we waited a pretty long time on that one
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