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Remove all uses of compare_trees and replace with Tree.changes_from throughout bzrlib.

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doc/library-interface.txt
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*****************
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Library interface
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*****************
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Should have a pleasant library interface.
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* Be clear what is supposed to be in a stable public interface and
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  what is not.  (A common failing of Python programs.)
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* If a function changes the working directory (as may be necessary to
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  run patch) it should restore it.