GH-2254: Compaction using a temporary directory and atomic move

[afs]

GitHub issue resolved #2254

Pull request Description:

Use a temporary directory for building the compacted storage. Clear-up any stray temporary directories when creating the Java objects for the database.

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• [x] Tests are included.
• [x] Commits have been squashed to remove intermediate development commit messages.
• [x] Key commit messages start with the issue number (GH-xxxx)

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See the Apache Jena "Contributing" guide.