Here are some questions and answers which may be of use. The first section is a jump table to the actual questions.
This list should be fairly short.
General
Troubleshooting
Yes. This project is regularly synced with the master branch but it really depends on my schedule.
You can find my fork here.
git clone git://github.com/nwind21/ardupilot.git C:\<your git working root>\nwind21\ardupilot
I use a Vagrant with Puppet provisioned 12.04 Precise 32 on a Lenovo Yoga i7 laptop with VTX enabled for multi-core support.
For editing I use: Notepad++, Eclipse
For documentation and this site, I use Jekyll.
This can be a few things:
You probably have VirtualBox version 4.3.10 and installed the Guest Additions.
/home/vagrant/vbox_patch.sh
and restart your machine using vagrant reload