swap `file:list_dir` for `file:list_dir_all` due to nonexistence of latter prior to r16x

(in `rebar_file_utils`)

- Includes tests for templates and their application

Now supports arbitrary commands

- Adding tests for package deps
- Adding conflict/override warnings for package deps
- Adding cycle detection for packages
- Adding cycle detection for mixed packages+source
- Fixing internal dependency format of package resources when converted
  to rebar_app_info
- normalizing level-order prioritization to be based on lexicographical
  sort of app names rather than traversal order (which is undefined for
  package deps)
- Fixing tests for source deps for deep cycle detection
- Fixing bugs with source deps
- Relaxed version format checks for test utils

A lot of fixes are combined in there because I didn't want to commit
non-passing code, and many bugs were found when adding the second batch
of tests as part of the original effort.

The case in mind here is due to conflicts, and tests have been added for
this.

- Adding tests
- fixing use of set fetching to find repeated deps and prevent infinite
  loops

On a circular loop rebar3 now fails with `{error, no_sort}`, which is
uncaught and should be handled to consider the issue fully fixed.

- Reworked the helpers for existing suites and expanded them
- Created a mock git resource module to test for its dependency fetching
- Added a test suite for dependency resolving with first checks for
  common cases (https://gist.github.com/ferd/197cc5c0b85aae370436)

Left to do would include:

- Verify warnings
- Verify failures
- Verify dependency updates resolving

As mentioned in the OTP documentation, licensed customers may use
patched OTP installations where the otp_patch_apply tool adds a '**'
suffix as a flag saying the system consists of application versions from
multiple OTP versions. When we get such a version string, we drop the
suffix, as we cannot obtain relevant information from it as far as
tooling is concerned.

Augment 'tests' option of 'rebar eunit' command with ability to specify
tests to run using module-qualified names. This change also forced me
to change the way modules for coverage and for testing itself are
selected - module-qualified tests specifications are now taken into
consideration. Extend tests to cover new functionality. Update
dialyzer_reference accordingly.

While at it, improve the error message printed by rebar_utils:sh/2.

Allow rebar to compile applications using Erlang/OTP 17 and older
versions.  This patch only provides partial support since the rebar
tool itself must be compiled using an Erlang/OTP version that is older
than 17.

It is a portable version of the realpath(1) utility that you can find on
Mac OS X and FreeBSD (see also The Open Group Base Specifications Issue
6, IEEE Std 1003.1).

Without the -P flag, pwd(1) might return different values when the
current path contains one or more symlinks, depending on how you got
into the current directory.

In simplenode.runner, this may cause PIPE_DIR to have different values
on each use, which will make it impossible to connect to the running
node unless you guess the correct path yourself.

* Allow the following predefined analyses :
   undefined_function_calls, undefined_functions, locals_not_used,
   exports_not_used, deprecated_function_calls, deprecated_functions

* Trap some possible errors in case module information is not
    available

* ignore_xref works on all checks and can take {M,F,A} tuples.
  (Automatic behaviour export suppression still only works on
  exports_not_used)

Running tests on windows creates false positive due to setup failures
not executing all tests.  Checking for tmp_dir was failing on
subsequent runs.  Added cases to tmp_dir creation to delete preexisting
tmp_dirs in .eunit directory.

This change fixes #310.

This patch corrects the vm.args behavior while building upgrade tarballs
by copying the file from the release into the upgrade. Additionally it
patches the dummy runner script in the upgrade test project to work
properly.

app.config has been a long standing erroneous file in rebar. Erlang/OTP
documentation suggests a sys.config file instead. This file is stored in
the releases/VSN directory. This does a few things but most importantly
it ensures your config (contained in the application environment)
survives a hot upgrade. It also has the advantage of allowing the
configuration of the application to be versioned along side the
application code. This patch flips rebar to use sys.config rather than
app.config.

Additionally it makes this flip to vm.args as well, making them
versioned just like sys.config.

This patch also includes runner script changes to support the old
etc/app.config config file location and support for Windows.

Thanks to mokele for the initial work and kick in the pants to make this
finially happen.