You can clone with
HTTPS or Subversion.
There are lots of popular nodejs modules (e.g. express, less, jade) that install symlinks in node_modules/.bin that point back to the bin subdirectory in their respective subtree.
Currently vmc update complains about them due to a failure in understanding the symlink structure:
Error: Can't deploy application containing links '/Users/davida/src/foo/node_modules/.bin/jade' that reach outside its root '/Users/davida/src/foo'
I suspect the root bug is the fact that the symlink is assessed to reach outside its root, even though it clearly isn't:
Thanks. I had this same problem, trying to follow the instructions in the tutorial (link below), which being from 9 months ago, used npm bundle. The vmc I downloaded today did not have the fix yet.