Submodule extensions

new config file locations and defaults

As of git v1.7.12, $HOME/.config/git/ is supported as a new
location for "config", "attributes", and "ignore" files.

Depending on what you had done before adding new items to the
internal ignores list, it was possible for the cache of ignore
data to be uninitialized.

Just clean up valgrind warnings about uninitialized memory
and also clear out errno in some cases where it results in
a false error message being generated at a later point.

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`.

Add git_repository_init_ext for power initters

This cleans up a number of items suggested during code review
with @vmg, including:

* renaming "outside repo" config API to `git_config_open_default`
* killing the `git_config_open_global` API
* removing the `git_` prefix from the static functions in fileops
* removing some unnecessary functionality from the "cp" command

If you use the clar cleanup callback function, you can't pass a
reference pointer to a stack allocated variable because when the
cleanup function runs, the stack won't exist anymore.

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.

The extended version of repository init adds support for many
of the things that you can do with `git init` and sets up
structures that will make it easier to extend further in the
future.

In looking at PR #878, I found a few small bugs in the diff code,
mostly related to work that can be avoided when processing tree-
to-tree diffs that was always being carried out.  This commit has
some small fixes in it.

API for managing in-memory ignore rules

This fills out the ignore API and adds tests.

This creates a public API for adding to the internal ignores
list, which already existing but was not accessible.

This adds the new default value for core.excludesfile also.

Filemode enum

Avoids getting ERROR_SHARING_VIOLATION on win32
and killing the entire clar run.

Make the memory-window conrol structures global

Up to now, the idea was that the user would do all the operations for
one repository in the same thread. Thus we could have the
memory-mapped window information thread-local and avoid any locking.

This is not practical in a few environments, such as Apple's GCD which
allocates threads arbitrarily or the .NET CLR, where the OS-level
thread can change at any moment.

Make the control structure global and protect it with a mutex so we
don't depend on the thread currently executing the code.

Handling of 100664 deprecated mode in tree entries

Clone

Minor fixes

Return -1 to stop the iteration instead of not-0

git_tree_walk callback return value semantic does not match documentation