Ensure reuc vector is always valid

In theory, if there was a problem reading the REUC data, the
read_reuc() routine could have left uninitialized and invalid
data in the git_index vector.  This moves the line that inserts a
new entry into the vector down to the bottom of the routine so we
know all the content is already valid.  Also, per @linquize, this
uses calloc to ensure no uninitialized data.

Use calloc() for safety

Fetch should not fail when remote HEAD reference is not present locally

Index entry dup and free

Move the git_index_entry to the very top, since it provides the
main structure that needs to be understood by the reader, then
move the bitmasks for the flags and the flags_extended under that
since they are details for looking at particular fields of the
structure.

This removes the functions to duplicate and free copies of a
git_index_entry and updates the comments to explain that you
should just use the public definition of the struct as needed.

This adds git_index_entry_dup to make a copy of an existing entry
and git_index_entry_free to release the memory of the copy.  It
also updates the documentation for git_index_get_bypath and
git_index_get_byindex to make it clear that the returned structure
should *not* be modified.

The constants for extracting data from git_index_entry flags and
flags_extended are not named in a way that makes it easy to know
where to use each one.  This improves the docs for the flags (and
slightly reorganizes them), so it should be more obvious.

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.