ls-files: rework exclude patterns.

Pasky and others raised many valid points on the problems
initial exclude pattern enhancement work had.  Based on the
list discussion, rework the exclude logic to use "last match
determines its fate" rule, and order the list by exclude-from
(the fallback default pattern file), exclude-per-directory
(shallower to deeper, so deeper ones can override), and then
command line exclude patterns.

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

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