What does the message "rewrite ... (90%)" after a Git commit mean?

Its a measure of the similarity index. The similarity index is the percentage of unchanged lines. git thinks your file is text.

I believe Martin is correct, that number is the similarity index. From the git-diff man pages:

The similarity index is the percentage of unchanged lines, and the dissimilarity index is the percentage of changed lines. It is a rounded down integer, followed by a percent sign. The similarity index value of 100% is thus reserved for two equal files, while 100% dissimilarity means that no line from the old file made it into the new one.

First time I saw the number I thought my binaries were changing dramatically!.