Use index-filter instead of tree-filter in graduate.sh

tree-filter causes git-filter-branch to checkout current tree for every
commit. That's rather IO-expensive operation. Given that tree-filter
runs "git rm" for every unneeded file, IO load becomes even higher.

With this change graduate.sh becomes less IO-bound and so runs way
faster (over 10x faster on my machine, even with tmpfs).

Change-Id: I3f08a3ac9a7f99a22b58c0c8017a53f4420fdcc3
Merge "Use index-filter instead of tree-filter in graduate.sh"