read-tree, merge-recursive: overwrite ignored files by default

read-tree, merge-recursive: overwrite ignored files by default

This fixes a long-standing patchwork of ignored files handling in
read-tree and merge-recursive, called out and suggested by Junio long
ago.  Quoting from commit dcf0c16ef1 ("core.excludesfile clean-up"
2007-11-16):

    git-read-tree takes --exclude-per-directory=<gitignore>,
    not because the flexibility was needed.  Again, this was
    because the option predates the standardization of the ignore
    files.

    ...

    On the other hand, I think it makes perfect sense to fix
    git-read-tree, git-merge-recursive and git-clean to follow the
    same rule as other commands.  I do not think of a valid use case
    to give an exclude-per-directory that is nonstandard to
    read-tree command, outside a "negative" test in the t1004 test
    script.

    This patch is the first step to untangle this mess.

    The next step would be to teach read-tree, merge-recursive and
    clean (in C) to use setup_standard_excludes().

History shows each of these were partially or fully fixed:

  * clean was taught the new trick in 1617adc7a0 ("Teach git clean to
    use setup_standard_excludes()", 2007-11-14).

  * read-tree was primarily used by checkout & merge scripts.  checkout
    and merge later became builtins and were both fixed to use the new
    setup_standard_excludes() handling in fc001b526c ("checkout,merge:
    loosen overwriting untracked file check based on info/exclude",
    2011-11-27).  So the primary users were fixed, though read-tree
    itself was not.

  * merge-recursive has now been replaced as the default merge backend
    by merge-ort.  merge-ort fixed this by using
    setup_standard_excludes() starting early in its implementation; see
    commit 6681ce5cf6 ("merge-ort: add implementation of checkout()",
    2020-12-13), largely due to its design depending on checkout() and
    thus being influenced by the checkout code.  However,
    merge-recursive itself was not fixed here, in part because its
    design meant it had difficulty differentiating between untracked
    files, ignored files, leftover tracked files that haven't been
    removed yet due to order of processing files, and files written by
    itself due to collisions).

Make the conversion more complete by now handling read-tree and
handling at least the unpack_trees() portion of merge-recursive.  While
merge-recursive is on its way out, fixing the unpack_trees() portion is
easy and facilitates some of the later changes in this series.  Note
that fixing read-tree makes the --exclude-per-directory option to
read-tree useless, so we remove it from the documentation (though we
continue to accept it if passed).

The read-tree changes happen to fix a bug in t1013.

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