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 refactors the diff output code so that an iterator object
can be used to traverse and generate the diffs, instead of just
the `foreach()` style with callbacks.  The code has been rearranged
so that the two styles can still share most functions.

This also replaces `GIT_REVWALKOVER` with `GIT_ITEROVER` and uses
that as a common error code for marking the end of iteration when
using a iterator style of object.

This extends git_repository_init_ext further with support for
initializing the repository from an external template directory
and with support for the "create shared" type flags that make a
set GID repository directory.

This also adds tests for much of the new functionality to the
existing `repo/init.c` test suite.

Also, this adds a bunch of new utility functions including a
very general purpose `git_futils_mkdir` (with the ability to
make paths and to chmod the paths post-creation) and a file
tree copying function `git_futils_cp_r`.  Also, this includes
some new path functions that were useful to keep the code
simple.

Clone

The config file parser was not working right if there was no
whitespace between the value name and the equals sign.  This
fixes that.