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

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.

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:

064195dc5a (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.

CONTRIBUTING: apply stylistic change suggested by dizzyd

Always return the errors and warnings from erlydtl

Fix eunit regression introduced in 2716d83a18

Extract contributing guide into CONTRIBUTING.md

This allows us to use `rebar_base_compiler:ok_tuple/3` and
`rebar_base_compiler:error_tuple/5` when returning from
`rebar_erlydtl_compiler`.

While at it, refactor the guide for clarity. Some of the new text was
taken from erlware/relx/CONTRIBUTING.md and modified as needed.

Use alternative way to detect net_kernel:stop/0 has succeeded as
suggested by Ulf Wiger.

The order in which modules, within an application, are loaded can be
important. This patch adds allows the specification of module
dependencies such that generate .appup/.relup scripts will load a
module's dependent modules before itself.

To use:

in rebar.config, add a module_deps

{module_deps, [{ModuleName, [DependentModuleName, ...]}]}.

ModuleName is the name of any module, followed by a list of module
names that it depends on.

Fix typo in neotoma help message

mib_to_hrl compilation verbosity via 'mib_opts'

let vm.args and sys.config as optional

Support conditional template instructions

Change rebar_ct:check_log/3 to use double quotes

The call to the grep program in rebar_ct:check_log/3 used single
quotation marks around the strings grep should search for. This works
well in most cases but fails on Windows 7 using GNU grep 2.5.4 as
installed by the Chocolatey package GnuWin 0.6.3.1 with the follow
message:

ERROR: cmd /q /c grep -e 'TEST COMPLETE' -e '{error,make_failed}'
ct/raw.log
failed with error: 2 and output:
grep: COMPLETE': No such file or directory

This commit changes the single quotation marks to double quotation
marks. I've tested this using GNU grep 2.5.3 on a Debian Linux machine
and it works well.

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.

Previously, the configuration setting 'mib_opts' in rebar.config
would affect the call to snmpc:compile/2, so that (for example)
verbosity could be controlled.  However, the subsequent call to
snmpc:mib_to_hrl/1 did not include any of these options, so it
did not appear to be possible to control the verbosity of the
process of converting a MIB to a .hrl file.  To make matters
worse, the default was to dump a full trace -- including debug
output and various logging -- so the act of compiling a large
number of MIBs could result in a huge amount of "noisy" output
that hid any signal (meaningful warnings, errors, etc.).

This commit addresses that issue by replacing the call to
snmpc:mib_to_hrl/1 with a call to snmpc:mib_to_hrl/3 instead,
which includes an "options" argument that, at present, is only
capable of setting verbosity.  The verbosity setting is taken
from the 'mib_opts' setting in rebar_config, if present, and
the approriate kind of argument is passed to snmpc:mib_to_hrl/3.

It should be noted that snmpc:mib_to_hrl/3 is not listed in
Erlang's documentation, but does appear in the list of "API"
exports at the top of snmpc.erl in R15B01 (and remains that way
in R16B01), so this appears to be more of a documentation oversight
than the use of a deep, dark function call that was not intended
to be public.  snmpc:mib_to_hrl/3 accepts an #options{} record
(defined in lib/srdlib/include/erl_compile.hrl within Erlang's
source distribution), though most of the fields in that record
are ignored by snmpc:mib_to_hrl/3; only verbosity can be controlled
this way.

To avoid problems with REMSH node being visible from another nodes
starts it in hidden mode (erl -hidden).

When a node is configured with -sname in app.config or sys.config the
REMSH_NAME_ARG and REMSH_REMSH_ARG arguments are incorrect due the
assumption that the node name always contains '@'.

To fix the bug, the script tries to find '@' and then compose the
arguments acording to node name type. If in long name mode the
script can't compose a correct node name exits with warning.

dialyzer_reference plus one minor patch

Document 'rebar help <CMD1> <CMD2>'

change cover html generation to produce valid html

Fixes and updates

- restore support for "rebar help xref"
- update rebar.config.sample
- update 'help xref' string
- simplify new/changed functions by breaking out code or
  using simpler syntax where applicable

- refactor plugin dirs code to be simpler and easier to read
- use erlang-mode's default (%%) comments for portability/consistency
- make sure erlang-mode's indenter is used so that a future whole
  buffer indent doesn't get messed up

Also fix a single line exceeding max column.

Add one more "unicode" option in expand_env_variable—I have a bullet in my prompt that was blowing it up