* Rework GIT_DIRREMOVAL values to GIT_RMDIR flags, allowing
  combinations of flags
* Add GIT_RMDIR_EMPTY_PARENTS flag to remove parent dirs that
  are left empty after removal
* Add GIT_MKDIR_VERIFY_DIR to give an error if item is a file,
  not a dir (previously an EEXISTS error was ignored, even for
  files) and enable this flag for git_futils_mkpath2file call
* Improve accuracy of error messages from git_futils_mkdir

Added `struct git_config_entry`: a git_config_entry contains the key, the value, and the config file level from which a config element was found.
Added `git_config_open_level`: build a single-level focused config object from a multi-level one.

We are now storing `git_config_entry`s in the khash of the config_file

This started as a complex new test for checkout going through the
"typechanges" test repository, but that revealed numerous issues
with checkout, including:

* complete failure with submodules
* failure to create blobs with exec bits
* problems when replacing a tree with a blob because the tree
  "example/" sorts after the blob "example" so the delete was
  being processed after the single file blob was created

This fixes most of those problems and includes a number of other
minor changes that made it easier to do that, including improving
the TYPECHANGE support in diff/status, etc.

When `git_submodule` became an opaque structure, I forgot to add
accessor functions for the fetchRecurseSubmodules config setting.
This fixes that.

This should confirm that issue #835 is fixed where a submodule that
is only declared in the .gitmodules file was not accessible via the
submodule APIs.

This is a big redesign of the git_submodule_status API and the
implementation of the redesigned API.  It also fixes a number of
bugs that I found in other parts of the submodule API while
writing the tests for the status part.

This also fixes a couple of bugs in the iterators that had not
been noticed before - one with iterating when there is a gitlink
(i.e. separate-work-dir) and one where I was treating anything
even vaguely submodule-like as a submodule, more aggressively
than core git does.

This fixes up a number of problems flagged by valgrind and also
cleans up the internal `git_submodule` allocation handling
overall with a simpler model.

This replaces the old submodule API with a new extended API that
supports most of the things that can be done with `git submodule`.