Make update-deps traverse deps breadth-first, top-down

This ensures that deps of deps are updated AFTER the dep listing them
is, so that a complicated project with many layers of deps will be
updated correctly. Any new deps encountered along the way are also
cloned, and THEIR deps are also evaluated.

Also added was conflict detection, if a dep has differing versions or
source information, inherited from different places, that will be logged
at the end of update-deps, along with the origin of each conflicting
dep.
Ignore skip_deps during update-deps as it has no meaning
Change how update-deps updates a git branch

Previously, update-deps on a dep tagged as {branch, ...} would do the
following:

  git fetch
  git checkout -q origin/<branch>

If you were already on that branch, the repo would end up in detached
head state. This is kind of annoying if you're doing local development.

This patch changes the behaviour to be

  git fetch
  git checkout -q <branch>
  git pull --ff-only --no-rebase -q <branch>

The intent of this is to move the branch's HEAD forward to match
upstream without destroying any local commits or changes, and without
accidentally causing merges or rebases. It will fail if the operation
can not be performed without losing history, merging or rebasing.

The previous behaviour has been around a very long time:

https://github.com/rebar/rebar/commit/064195dc5a90f5b0cc3ae92e8373671b0043033f#L0R308

It also exactly mirrors the download_source case, which is not really
true. With git tags and SHAs, one can assume that they don't change, but
branches move all the time.
Make update-deps honor apps= and skip_apps=

Because rebar_core handles skipping apps, we had to specialcase the
handling in the case of update-deps because it has to do its own dep
handling. The way this was done is not particularly clean, but there
currently does not exist another way for a command to signal rebar_core
that it doesn't want rebar_core to pay attention to skip_apps.

With this change, however, you can update-deps even with local
conflicting changes/commits by simply skipping the deps you don't wish
to update, or whitelisting he ones you do wish to update.
Fix skip check for deps not present
Address review comments and add inttest for update-deps
Typo
Merge pull request #142 from Vagabond/adt-update-deps

Make update-deps traverse deps breadth-first, top-down