External deps_dir should have higher priority than the config one

The external deps_dir should have higher priority because
it is used by scripts and other build tools to set up the
location of the dependencies. This commit ensures that,
even if a project has set deps_dir in its config file has
lower preference than the command line one.
Merge pull request #100 from josevalim/patch-1

External deps_dir should have higher priority than the config one