Log errors instead of stdout/stderr, no more System.exit(), update Maven Shade.

*   Made jannovar messages go to log instead of stdout/stderr, and removed
    all System.exit(...) calls.  Now if Jannovar errors out, it won't
    bring down the server (however, it will abort/cancel a variant import
    job).
*   Updated Maven Shade plug-in.
    There seems to be an issue with Maven 3.1+ and `maven-shade-plugin:2.0`.
    When running `mvn install`, the following error is encountered:

        [ERROR] Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:2.0:shade (default)
        Execution default of goal org.apache.maven.plugins:maven-shade-plugin:2.0:shade failed:
        A required class was missing while executing org.apache.maven.plugins:maven-shade-plugin:2.0:shade: org/sonatype/aether/version/VersionConstraint

    Updating `maven-shade-plugin` to 2.1 fixes the build.

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