Update links and urls in README.md.

README.md

 Mojo
 ====
 
 Mojo is an effort to extract a common platform out of Chrome's renderer and
 plugin processes that can support multiple types of sandboxed content, such as
 HTML, Pepper, or NaCl.
 
 ## Set-up and code check-out
 
 The instructions below only need to be done once. Note that a simple "git clone"
@@ skipping 166 matching lines @@
 `--no-config-file` to `mojo_run`.
 
 ### More examples
 
 Some applications can be run directly from the source tree. The development
 server serves the `src` directory, allowing to refer to these apps. For
 instance, this command serves a dart Mojo app from the source at
 `examples/dart/device_info/main.dart`:
 
 ```sh
-mojo_run https://core.mojoapps.io/examples/dart/device_info/main.dart [--android]
+mojo/devtools/common/mojo_run https://core.mojoapps.io/examples/dart/device_info/lib/main.dart [--android]
 ```
 
 Some applications are meant to be run embedded in a **window manager**. To run
 these, you can pass the app url using the `--embed` flag. This will run the
 window manager and pass the given url to it:
 
 ```sh
-devtools/common/mojo_run --embed https://core.mojoapps.io/ganesh_app.mojo [--android]
+mojo/devtools/common/mojo_run --embed https://core.mojoapps.io/ganesh_app.mojo [--android]
 ```
 
-By default, `mojo_run` uses https://core.mojoapps.io/kiosk_wm.mojo as the window
+By default, `mojo_run` uses mojo:kiosk_wm as the window
 manager. You can pass a different window manager url using the
 `--window-manager` flag to override this.
 
 For additional information on `mojo_run` refer to the built-in help and the
-[documentation](https://github.com/domokit/devtools/blob/master/README.md#runner).
+[documentation](mojo/devtools/common/docs/mojo_run.md).
 You can also request more information on what the tool is doing for you by
 passing the `--verbose` flag.
 
 ### <a name="debugging"></a>Debugging, tracing, profiling
 
 Devtools `mojo_debug` allows you to interactively inspect a running shell,
 collect performance traces and attach a gdb debugger.
 
 For additional information refer to the built-in help and the
-[documentation](https://github.com/domokit/devtools/blob/master/README.md#debugger).
+[documentation](mojo/devtools/common/docs/mojo_debug.md).
 
 ### Android set-up
 
 #### Adb
 
 For the Android tooling to work, you will need to have `adb` in your PATH. For
 that, you can either run:
 ```
 source build/android/envsetup.sh
 ```
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 making your first change: [C++ in Chromium
 101](http://dev.chromium.org/developers/cpp-in-chromium-101-codelab).
 
 To land a change after receiving LGTM:
 ```
 $ git cl land
 ```
 
 Don't break the build! Waterfall is here:
 http://build.chromium.org/p/client.mojo/waterfall