An earlier change to optimize directory-file conflict check
broke what "read-tree --emu23" expects.  This is fixed by this
commit.

(1) Introduces an explicit flag to tell add_cache_entry() not to
    check for conflicts and use it when reading an existing tree
    into an empty stage --- by definition this case can never
    introduce such conflicts.

(2) Makes read-cache.c:has_file_name() and read-cache.c:has_dir_name()
    aware of the cache stages, and flag conflict only with paths
    in the same stage.

Signed-off-by: Junio C Hamano <junkio@cox.net>
Signed-off-by: Linus Torvalds <torvalds@osdl.org>