read-tree: further loosen "working file will be lost" check.

read-tree: further loosen "working file will be lost" check.

This follows up commit ed93b449 where we removed overcautious
"working file will be lost" check.

A new option "--exclude-per-directory=.gitignore" can be used to
tell the "git-read-tree" command that the user does not mind
losing contents in untracked files in the working tree, if they
need to be overwritten by a merge (either a two-way "switch
branches" merge, or a three-way merge).

Signed-off-by: Junio C Hamano <junkio@cox.net>