added StagingDatabase.getAllPresentStagingOnly for the cases where it is known that only the staging db needs to be queried.
Use StagingDatabase.getAllStagingOnly in DeepMove if appropriate
Rename ObjectDatabase.getAll to getAllPresent to better align the method's name with its contract.
Change return type of ResolveGeogitDir from URL to Optional<URL>. It's bad practice for commands to return null.
Simplify getAllPresent() and deleteAll() for JEObjectDatabase. The extra complexity provided no real performance gain.
Do not print the percentage character if the progress is over it
add logger entries for org.geogit.osm and org.geotools
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