index: add failing test for clearing the mtime on read-tree

When we read a tree, we have no context for when a file was last
touched, and we should clear the mtime together with other fields.

This test adds the test for mtime as an example of what we should clear
if we want to match git behaviour.
index: don't keep any data from before the read-tree

When we're asked to read in a tree, we must leave many of the fields
zeroes. We should not be copying anything over from the old entries.