More tests (and fixes) for initializing repo from template

Disable ignore_case when writing the index to a tree

clear REUC on checkout

`git_diff_get_patch()` would unconditionally load the patch object and
then simply leak it if the user hadn't requested it. Short-circuit
loading the object if the user doesn't want it.

The rest of the plugs are simply calling the free functions of objects
allocated during the tests.

indexer: use a hashtable for keeping track of offsets

These offsets are needed for REF_DELTA objects, which encode which
object they use as a base, but not where it lies in the packfile, so
we need a list.

These objects are mostly from older packfiles, before OFS_DELTA was
widely spread. The time spent in indexing these packfiles is greatly
reduced, though remains above what git is able to do.

indexer: kill git_indexer

This was the first implementation and its goal was simply to have
something that worked. It is slow and now it's just taking up
space. Remove it and switch the one known usage to use the streaming
indexer.

Update contributing and conventions

When the examples/diff.c was written, there was not yet a revparse
API.  Now we can use it to make command line parsing way better
with less code.  Yay!

The discussion about converting some of our foreach-style APIs to
use iterator objects got me wanting to make a list of good starter
projects.  I put it in CONTRIBUTING.md and then went crazy with
updates to that file and to CONVENTIONS.md.

Allow empty config object and use it for tests

This removes assertions that prevent us from having an empty
git_config object and then updates some tests that were
dependent on global config state to use an empty config before
running anything.

Control for core.autocrlf during testing

Clone should not clean up directories it did not create

Why cdecl why?

This fixes some snprintf and vsnprintf related deprecation
warnings we've been having on Windows with recent compilers.

This removes the one-off GIT_CDECL and adds a new standard way of
doing this named GIT_STDLIB_CALL with a src/win32 specific def
when on the Windows platform.

Allows compilation in newer versions of MinGW that already defined it.

Add file similarity scoring to diff rename/copy detection

don't dereference at the end of the workdir iterator

When creating files, instead of actually using GIT_FILEMODE_BLOB
and the other various constants that happen to correspond to
mode values, apparently I should be just using 0666 and 0777, and
relying on the umask to clear bits and make the value sane.

This fixes the rules for copying a template directory and fixes
the checks to match that new behavior.  (Further changes to the
checkout logic to follow separately.)

Win32: Use constants in version resource definitions where possible

Signed-off-by: Sven Strickroth <email@cs-ware.de>

The new tests were not taking core.filemode into account when
testing file modes after repo initialization.  Fixed that and some
other Windows warnings that have crept in.

When PR #1359 removed the hooks from the test resources/template
directory, it made me realize that the tests for
git_repository_init_ext using templates must be pretty shabby
because we could not have been testing if the hooks were getting
created correctly.

So, this started with me recreating a couple of hooks, including
a sample and symlink, and adding tests that they got created
correctly in the various circumstances, including with the SHARED
modes, etc.  Unfortunately this uncovered some issues with how
directories and symlinks were copied and chmod'ed.  Also, there
was a FIXME in the code related to the chmod behavior as well.

Going back over the directory creation logic for setting up a
repository, I found it was a little difficult to read and could
result in creating and/or chmod'ing directories that the user
almost certainly didn't intend.

So that let to this work which makes repo initialization much
more careful (and hopefully easier to follow).  It required a
couple of extensions / changes to core fileops utilities, but I
also think those are for the better, at least for git_futils_cp_r
in terms of being careful about what actions it takes.

Increment reference counter in git_repository_set_config

This fixes #1365

Give props to Martin Pool

Martin Pool was the original author of the code referenced in the clone
example. Make note that he's given his permission and also give him the
proper credit.