Most of the other platforms have the runner code in a runner/ subdirectory; I meant to go back and do that for Linux, but didn't get to it. We should move the source for consistency, and to make the linux/ folder more organized. As part of that, we can move the application-specific part of the CMakeLists.txt into that folder, which makes the build rules easier to navigate.

This won't be a breaking change, because apps made with the old template will still work. But we should do it ASAP to reduce the number of people with different directory structures in the wild since it'll be a little confusing for people looking at other projects, answering questions about where to change things in native code, etc.

@robert-ancell If you have time to do this that would be great, otherwise I can probably do it.