Fixes GH-39: -d flag not working

It appears how I was handling the proc for the dockerfiles_path option was causing user input to be ignored. This commit fixes this issue.
Fixes #38 - Duplicate cookbook defs in Berksfile

If a cookbook appeared more than once in the runlist, it would appear that many times in the Berksfile. Also, the Berksfile wasn't being generated if you had no runlist even if you requested it be generated.
Merge branch 'tduffield/GH-38-39' into release/0.2.x
include_credentials now appends --no-remove-secure

As pointed out by Andrew Hsu, the initial process of removing the secure directory resulted in an intermediate layer with the credentials still in it. This process will now strip out the credentials within the same layer.
add .gitignore file that ignores secure files
Add secure_dir option

When a directory is specified with --secure-dir, knife-container will use that directory as the secure directory for the build. This will allow users to avoid commiting their secure directory to source control and support use in CI systems.
cleanup docker_init specs
Support private registry dockerfile names
use knife config for default base image in init

Allow people to specify alternate default base_image
first draft of container rebuild - commit to test
Add support for berksfile_source config
Add documentation about existing knife config
Handle image deletion and tagging appropriately
Fix bug with berksfile_source context variable

A default value was not being set nor was the value being properly accessed.
Update CHANGELOG
generate berksfile even with empty runlist
use mkmf to see if berks is installed
add new helper and base modules
add require and include statements for base class
use ruby 1.9 hash syntax