Initial support for transactions.
adapt remaining classes to the transaction work
make Index and WorkingTree independent of Repository, they only need a CommandLocator. Also use constructor injection instead of field injection.
working on RefDatabaseDecorator for transactions
Transaction refactor.
Removed dependencies on GeogitTransaction.
Added StagingArea, WorkingTree, and RefDatabase members to AbstractGeogitOp in order to facilitate overriding those classes by transactions.
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clean diffworktree javadocs