Seems from your messages that no files are downloaded yet from the repositories to your local system.
I've found TortoiseHg Workbench, provided in the virtual machine, very useful for managing my local files. I hadn't used it before so I also saw some messages like those when I first got started. There is a learning curve, but it's well worth the time. Try the Help menu there. Path, Synchronize, Update, and Graph interpretation are the really critical to keep your local code updated and add new code from the repositories. It's a snap once you see how it works!
One you've used "Update" to get your code up to the Revision you want, then you want to use Eclipse, particularly if you're working the firmware, to Clean and then Build Project. Both TortoiseHg and Eclipse are provided pre-configured, so you can use them straight away on the Bitcraze repositories.
Naturally, there are many things you can do without using these tools, but you'll need depth in using the Hg (Mercurial) command line options directly.
I'm just a noob at using these excellent tools and I"m sure others here are more capable of writing a better tutorial!
Still, I hope this helps point you in the right direction!
VGer's v1.7.1 frame, 10DOF Crazyflie, Wireless Xbox360 Controller, Virtual Machine on VMware/Windows 7