Perform some error checking when examining symlink directories.

 Native Git allows symlinked directories under .git/refs. This
 change allows libgit2 to also look for references that live under
 symlinked directories.

Signed-off-by: Andy Doan <andy@opensourcefoundries.com>

Next to including several files, our "common.h" header also declares
various macros which are then used throughout the project. As such, we
have to make sure to always include this file first in all
implementation files. Otherwise, we might encounter problems or even
silent behavioural differences due to macros or defines not being
defined as they should be. So in fact, our header and implementation
files should make sure to always include "common.h" first.

This commit does so by establishing a common include pattern. Header
files inside of "src" will now always include "common.h" as its first
other file, separated by a newline from all the other includes to make
it stand out as special. There are two cases for the implementation
files. If they do have a matching header file, they will always include
this one first, leading to "common.h" being transitively included as
first file. If they do not have a matching header file, they instead
include "common.h" as first file themselves.

This fixes the outlined problems and will become our standard practice
for header and source files inside of the "src/" from now on.

Remove some unused functions, refactor some ugliness.

Since the three iterators implement `advance_over` differently,
mandate it and implement each.

Now that iterators do not return `GIT_ENOTFOUND` when advancing
into an empty directory, we do not need a special `advance_into_or_over`
function.

Drop some of the layers of indirection between the workdir and the
filesystem iterators.  This makes the code a little bit easier to
follow, and reduces the number of unnecessary allocations a bit as
well.  (Prior to this, when we filter entries, we would allocate them,
filter them and then free them; now we do the filtering before
allocation.)

Also, rename `git_iterator_advance_over_with_status` to just
`git_iterator_advance_over`.  Mostly because it's a fucking long-ass
function name otherwise.

Refactored the tree iterator to never recurse; simply process the
next entry in order in `advance`.  Additionally, reduce the number of
allocations and sorting as much as possible to provide a ~30% speedup
on case-sensitive iteration.  (The gains for case-insensitive iteration
are less majestic.)

Disambiguate the reset and reset_range functions.  Now reset_range
with a NULL path will clear the start or end; reset will leave the
existing start and end unchanged.