Fix vagrant build issues with submodules.

Tools/vagrant/initvagrant.sh

@@ -46,6 +46,9 @@ exportline="export PATH=/opt/$ARM_ROOT/bin:\$PATH"
 if grep -Fxq "$exportline" /home/vagrant/.profile; then echo nothing to do ; else echo $exportline >> /home/vagrant/.profile; fi
 
 echo "source /vagrant/Tools/vagrant/shellinit.sh" >>/home/vagrant/.profile
+# This allows the PX4NuttX build to proceed when the underlying fs is on windows
+# It is only marginally less efficient on Linux
+echo "export PX4_WINTOOL=y" >>/home/vagrant/.profile
 ln -fs /vagrant/Tools/vagrant/screenrc /home/vagrant/.screenrc
 
 # build JSB sim

Vagrantfile

@@ -25,15 +25,19 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
       vb.customize ["modifyvm", :id, "--memory", "2048"]
       vb.customize ["modifyvm", :id, "--ioapic", "on"]
       vb.customize ["modifyvm", :id, "--cpus", "2"]
-      # NuttX needs symlinks. If you want to go that route you need this setting, but rsync is easier. 
-#      vb.customize ["setextradata", :id, "VBoxInternal2/SharedFoldersEnableSymlinksCreate/PX4NuttX", "1"]
       # Make some effort to avoid clock skew
       vb.customize ["guestproperty", "set", :id, "/VirtualBox/GuestAdd/VBoxService/--timesync-set-threshold", "5000"]
       vb.customize ["guestproperty", "set", :id, "/VirtualBox/GuestAdd/VBoxService/--timesync-set-start"]
       vb.customize ["guestproperty", "set", :id, "/VirtualBox/GuestAdd/VBoxService/--timesync-set-on-restore", "1"]
   end
 
-
+  # The created VM sets PX4_WINTOOL=y to allow builds to proceed using shared folders with using symlinks.
+  # However shared folders are quite slow. If you have rsync installed then this is a faster way of building.
+  # In addition there are problems with px4-clean when using shared folders. Using rsync avoids this.
+  # config.vm.synced_folder ".", "/vagrant", type: "rsync", rsync__auto: true
+  
+  # If you are on windows then you must use a version of git >= 1.8.x to update the submodules
+  # in order to build. Older versions of git use absolute paths for submodules which confuses things.
 
   config.vm.provision :shell, path: "Tools/vagrant/initvagrant.sh"  
 end