Move the `tree-diff` tool into ./tools, which is our new place for tools
used by the test-suite or during development.
The only hard-coded user is the TestBase, so fix its path to the tool
so the test-suite will continue to find it.
We need to know the exact difference of modified files in both trees.
Outputting the whole files into a diff might make a huge diff file,
therefore only their hashes are written.
