This commit fixes a bug where passing extra dependency entries
(using -fdepfile-entry) would result in -MP incorrectly emitting
a phony target for the input file, and no phony target for the
first extra dependency.
The extra dependencies are added first to the filename vector in
DFGImpl. That clashed with the emission of the phony targets, as
the code assumed that the first index always correspond to the
input file.
This is incorrect if there are duplicates in Opts.ExtraDeps. Also please update the test to have duplicate extra dependencies.