Cleaning up avocado build.

[fnothaft]

Various build cleanup:

• Split the main Avocado class into a cli module. Long term, we'll move all config out of the core module and into the cli module (see Separate config from variant calling algorithms #86). This resolves Avocado depends on ADAM-CLI #31, at least for now.
• Changed version 0.0.2 to 0.0.2-SNAPSHOT, and renamed main project to avocado-parent.
• Refactored dependencies in parent project into dependencyManagement.

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Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/avocado-prb/78/

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Merged build started.

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Merged build finished.

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Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/avocado-prb-matrix/1/

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Merged build triggered.

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Merged build started.

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Merged build finished. All automated tests passed.

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/avocado-prb-matrix/2/

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Merged build finished. All automated tests passed.

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/avocado-prb/79/