Bug fixes for checkout and diff

Fix trailing whitespaces

Since I added the GIT_IDXENTRY_STAGE macro to extract the stage
from a git_index_entry, we probably don't need an internal inline
function to do the same thing.

Under some strange circumstances, diffs can end up listing files
that we can't actually open successfully.  Instead of aborting
the git_diff_find_similar, this makes it so that those files just
won't be considered as valid rename/copy targets instead.

It is possible for there to be a submodule in a repository with
no .gitmodules file (for example, if the user forgot to commit
the .gitmodules file).  In this case, core Git will just create
an empty directory as a placeholder for the submodule but
otherwise ignore it.  We were generating an error and stopping
the checkout.  This makes our behavior match that of core git.

Unlike blob updates, symlink updates cannot be done "in place"
writing over an old symlink.  This means that in checkout when we
realize that we can safely update a symlink, we still need to
remove the old one before writing the new.

When the last item in a diff was an untracked directory that only
contained ignored items, the loop to scan the contents would run
off the end of the iterator and dereference a NULL pointer.  This
includes a test that reproduces the problem and a fix.

Unify whitespaces to tabs

CMake: vendor strings

Create directory for symlink before creating symlink

Fix some memory leaks

This helps us install multiple versions of the library side-by-side.

The code surrounding zlib bundling did not take into consideration
that ZLIB_LIBRARY gets cached, and assumed that FIND(ZLIB) would
always set ZLIB_FOUND, which does not hold true, as this variable
signifies that we have found the package and had to look at the
system, as its location was not cached.

Only use the bundled sources if the external zlib is neither
newly-found nor cached.

Fix refdb iteration early termination bug

There was a problem found in the Rugged test suite where the
refdb_fs_backend__next function could exit too early in some
very specific hashing patterns for packed refs.  This ports
the Rugged test to libgit2 and then fixes the bug.

Fix broken build when MSVC SDL checks is enabled

Introduce a refs iterator

If the backend doesn't provide support for it, the matching is done in
refdb on top of a normal iterator.

Nobody should ever be using anything other than ALL at this level, so
remove the option altogether.

As part of this, git_reference_foreach_glob is now implemented in the
frontend using an iterator. Backends will later regain the ability of
doing the glob filtering in the backend.

Selecting wether to list loose or packed references is not something
we want to support anymore, so remove a test for this.

This allows us to get a list of reference names in a loop instead of callbacks.

Improve ignore handling in git_status_file

Fix diff output for renames and copies

Fix some memory leaks

If you use rename detection, the renamed and copied files would
not show any text diffs because the function that decides if
data should be loaded didn't know which sides of the diff to
load for those cases.

This adds a test that looks at the patch generated for diff
entries that are COPIED or RENAMED.

The git_status_file API was doing a hack to deal with files that
are inside ignored directories.  The status scan was not reporting
any file in this case, so git_status_file would attempt a final
"stat()" call, and return IGNORED if the file actually existed.

On case-insensitive filesystems where core.ignorecase is set
incorrectly, this magic check can "succeed" and report a file
as ignored when it should actually return ENOTFOUND.

Now that we have the GIT_STATUS_OPT_RECURSE_IGNORED_DIRS, we can
use that flag to make sure that git_status_file() will look into
ignored directories and eliminate the hack completely, so we give
the correct error.