[MERGE] Fix PreviewTree.annotate

[Aaron Bentley]

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Hi all,

This patch fixes PreviewTree.annotate to work correctly when a file has
been altered in the transform.

It builds on the following patches:
http://bundlebuggy.aaronbentley.com/request/%3C4863D54C.4000509@aaronbentley.com%3E
http://bundlebuggy.aaronbentley.com/request/%3C4863D625.2080800@aaronbentley.com%3E

Aaron
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