Ignore Developer Studio metadata files

* Remove the setup.sh script since it is not necessary if the
  --recursive option is passed to git clone.
* Correct a URL in the README.md which points to the Developer Studio
  branch of mangOH where submodule usage was proposed.

Also remove an application definition from the mangOH Red
sdef for SPI testing since the application is not published.

Remove the .gitignore entires since they are no longer relevant after
switching from repo to submodules.

This app will be presented at the tutorial session at Sierra Wireless
Developer Day 2016.

GPIO 1 has been changed to an input with pullup to match the pullup on
the card itself.