There are inconsistencies in the way commands currently handle
the core.excludesfile configuration variable.  The problem is
the variable is too new to be noticed by anything other than
git-add and git-status.

 * git-ls-files does not notice any of the "ignore" files by
   default, as it predates the standardized set of ignore files.
   The calling scripts established the convention to use
   .git/info/exclude, .gitignore, and later core.excludesfile.

 * git-add and git-status know about it because they call
   add_excludes_from_file() directly with their own notion of
   which standard set of ignore files to use.  This is just a
   stupid duplication of code that need to be updated every time
   the definition of the standard set of ignore files is
   changed.

 * 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.

 * git-merge-recursive uses hardcoded per-directory .gitignore
   and nothing else.  git-clean (scripted version) does not
   honor core.* because its call to underlying ls-files does not
   know about it.  git-clean in C (parked in 'pu') doesn't either.

We probably could change git-ls-files to use the standard set
when no excludes are specified on the command line and ignore
processing was asked, or something like that, but that will be a
change in semantics and might break people's scripts in a subtle
way.  I am somewhat reluctant to make such a change.

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().

Signed-off-by: Junio C Hamano <gitster@pobox.com>