I was accidentally using a value that I had just freed.  This
moves the clearing of the delta internal flags into a better place.

This flips rename detection around so instead of creating a
forward mapping from deltas to possible rename targets, instead
it creates a reverse mapping, looking at possible targets and
trying to find a source that they could have been renamed or
copied from.  This is important because each output can only
have a single source, but a given source could map to multiple
outputs (in the form of COPIED records).

Additionally, this makes a couple of tweaks to the public rename
detection APIs, mostly renaming a couple of options that control
the behavior to make more sense and to be more like core Git.

I walked through the tests looking at the exact results and
updated the expectations based on what I saw.  The new code is
different from the old because it cannot give some nonsense
results (like A was renamed to both B and C) which were part of
the outputs previously.

This adds a bunch more rename detection tests including checks
vs the working directory, the new exact match options, some more
whitespace variants, etc.

This also adds a git_futils_writebuffer helper function and uses
it in checkout.  This is mainly added because I wanted an easy
way to write out a git_buf to disk inside my test code.

- Add new GIT_DIFF_FIND_EXACT_MATCH_ONLY flag to do similarity
  matching without using the similarity metric (i.e. only compare
  the SHA).
- Clean up the similarity measurement code to more rigorously
  distinguish between files that are not similar and files that
  are not comparable (previously, a 0 could either mean that the
  files could not be compared or that they were totally different)
- When splitting a MODIFIED file into a DELETE/ADD pair, actually
  make a DELETED/UNTRACKED pair if the right side of the diff is
  from the working directory.  This prevents an odd mix of ADDED
  and UNTRACKED files on workdir diffs.

Add --raw output format and (some) options to invoke rename/copy
detection on the diff.

There are a number of bugs in the rename code that only were
obvious when I started testing it against large old repos with
more complex patterns.  (The code to do that testing is not ready
to merge with libgit2, but I do plan to add more thorough tests.)

This contains a significant number of changes and also tweaks the
public API slightly to make emulating core git easier.

Most notably, this separates the GIT_DIFF_FIND_AND_BREAK_REWRITES
flag into FIND_REWRITES (which adds a self-similarity score to
every modified file) and BREAK_REWRITES (which splits the modified
deltas into add/remove pairs in the diff list).  When you do a raw
output of core git, rewrites show up as M090 or such, not at A and
D output, so I wanted to be able to emulate that.

Publicly, this also changes the flags to be uint16_t since we
don't need values out of that range.

Internally, this contains significant changes from a number of
small bug fixes (like using the wrong side of the diff to decide
if the object could be found in the ODB vs the workdir) to larger
issues about which files can and should be compared and how the
various edge cases of similarity scores should be treated.

Honestly, I don't think this is the last update that will have to
be made to this code, but I think this moves us closer to correct
behavior and I tried to document the code so it would be easier
to follow..

The delta cmp function needs to choose the correct path for
ordering when a delta is ADDED, RENAMED, or COPIED.

Makes it easier to emulate the --raw option

I frequently want to the the first N digits of an OID formatted
as a string and I'd like it to be efficient.  This function makes
that easy and I could rewrite the OID formatters in terms of it.

Add cat-file to examples (with some public API improvements)

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

This adds an example implementation that emulates git cat-file.
It is a convenient and relatively simple example of getting data
out of a repository.

Implementing this also revealed that there are a number of APIs
that are still not using const pointers to objects that really
ought to be.  The main cause of this is that `git_vector_bsearch`
may need to call `git_vector_sort` before doing the search, so a
const pointer to the vector is not allowed.  However, for tree
objects, with a little care, we can ensure that the vector of
tree entries is always sorted and allow lookups to take a const
pointer.  Also, the missing const in commit objects just looks
like an oversight.

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.