builtin/am: use apply API in run_apply()

This replaces run_apply() implementation with a new one that
uses the apply API that has been previously prepared in
apply.c and apply.h.

This shoud improve performance a lot in certain cases.

As the previous implementation was creating a new `git apply`
process to apply each patch, it could be slow on systems like
Windows where it is costly to create new processes.

Also the new `git apply` process had to read the index from
disk, and when the process was done the calling process
discarded its own index and read back from disk the new
index that had been created by the `git apply` process.

This could be very inefficient with big repositories that
have big index files, especially when the system decided
that it was a good idea to run the `git apply` processes on
a different processor core.

Also eliminating index reads enables further performance
improvements by using:

`git update-index --split-index`

For example here is a benchmark of a multi hundred commit
rebase on the Linux kernel on a Debian laptop with SSD:

command: git rebase --onto 1993b17 52bef0c 29dde7c

Vanilla "next" without split index:                1m54.953s
Vanilla "next" with split index:                   1m22.476s
This series on top of "next" without split index:  1m12.034s
This series on top of "next" with split index:     0m15.678s

(using branch "next" from mid April 2016.)

Benchmarked-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Signed-off-by: Christian Couder <chriscool@tuxfamily.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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