New FileSystem API

This pull request adds a new FileSystem API that replaces `NativeFileSystem`, `FileIndexManager` and direct calls to `brackets.fs.*` functions.

This pull request changes the API, but does not add any significant new features or performance gains. These will be done in subsequent pull requests. 

This is a big change. It _will_ break some extensions. However, the breakages are minimized through deprecation "shims" for many of the commonly used APIs that have been removed.

See [this Brackets-Dev forum thread](https://groups.google.com/forum/#!topic/brackets-dev/95PyDKfMO0M) for an introduction to the changes.

See the [FileSystem](https://github.com/adobe/brackets/wiki/File-System) and [FileSystem API Migration](https://github.com/adobe/brackets/wiki/File-System-API-Migration) wiki pages for more details.

Sign-offs:
- [x] @peterflynn 
- [x] @iwehrman 
- [x] @gruehle