1. Fix sort order problem with submodules where "mod" was sorting
after "mod-plus" because they were being sorted as "mod/" and
"mod-plus/". This involved pushing the "contains a .git entry"
test significantly lower in the stack.
2. Reinstate behavior that a directory which contains a .git entry
will be treated as a submodule during iteration even if it is
not yet added to the .gitmodules.
3. Now that any directory containing .git is reported as submodule,
we have to be more careful checking for GIT_EEXISTS when we
do a submodule lookup, because that is the error code that is
returned by git_submodule_lookup when you try to look up a
directory containing .git that has no record in gitmodules or
the index.
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 fixes up a number of problems flagged by valgrind and also
cleans up the internal `git_submodule` allocation handling
overall with a simpler model.
