Sync plugin's folder structure with core.

Looking at [cakephp/acl](https://github.com/cakephp/acl) it felt icky to see class file mixed with other metadata files at root. With this change plugins will have 3 top level folders `src`, `tests` and `webroot`.
Can do. `App::pluginPath()` can include the `src/` segment and we can keep `Plugin::path()` without it.