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Organize the on disk layout.

Also fix a few encoding issues.

In case you had not already noticed, this is a really big commit.
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1 parent b645fa0 commit b89081c18b63d4388b145d078215cfabb7264697 @dak180 dak180 committed Nov 22, 2012
Showing 1,662 changed files with 19,790 additions and 2,792 deletions.
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