stash: remove unnecessary process forking

When stash was converted from shell to a builtin, it merely
transliterated the forking of various git commands from shell to a C
program that would fork the same commands.  Some of those were converted
over to actual library calls, but much of the pipeline-of-commands
design still remains.  Fix some of this by replacing the portion
corresponding to

    git diff-index --cached --name-only --diff-filter=A $CTREE >"$a"
    git read-tree --reset $CTREE
    git update-index --add --stdin <"$a"
    rm -f "$a"

into a library function that does the same thing.  (The read-tree
--reset was already partially converted over to a library call, but as
an independent piece.)  Note here that this came after a merge operation
was performed.  The merge machinery always stages anything that cleanly
merges, and the above code only runs if there are no conflicts.  Its
purpose is to make it so that when there are no conflicts, all the
changes from the stash are unstaged.  However, that causes brand new
files from the stash to become untracked, so the code above first saves
those files off and then re-adds them afterwards.

We replace the whole series of commands with a simple function that will
unstage files that are not newly added.  This doesn't fix any bugs in
the usage of these commands, it simply matches the existing behavior but
makes it into a single atomic operation that we can then operate on as a
whole.  A subsequent commit will take advantage of this to fix issues
with these commands in sparse-checkouts.

This conversion incidentally fixes t3906.1, because the separate
update-index process would die with the following error messages:
    error: uninitialized_sub: is a directory - add files inside instead
    fatal: Unable to process path uninitialized_sub
The unstaging of the directory as a submodule meant it was no longer
tracked, and thus as an uninitialized directory it could not be added
back using `git update-index --add`, thus resulting in this error and
early abort.  Most of the submodule tests in 3906 continue to fail after
this change, this change was just enough to push the first of those
tests to success.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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