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Comprehensive build system is complete.

See merge request !2

bugfixes in refresh_shell. not sure if we can force the parent to refresh after install (/users/rberkheimer/library/java and  vars reference previous values, so in multiple installs, this path will be included twice).

simplified some installation scripts; added Makefile templates for user library building, added to install path; work on simplifying JAR contents through gradle build.

update installation targets for primary installation scripts to remove directory before making to ensure that it is clean.

completed initial installation-from-artifacts machinery, ready for testing. Don't forget to add instructions to the README after testing.

This commit marks the successful test of native sessions. Cleanup to be done now before adding automatic memory management of jobjects.