Fix initialization of repo directories

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.
Fix portability issues on Windows

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.
Make mode handling during init more like git

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.)
Clone should not delete directories it did not create
Merge pull request #1378 from jamill/clone_no_delete

Clone should not clean up directories it did not create
Control for core.autocrlf during testing
Disable ignore_case when writing the index to a tree
Merge pull request #1379 from arrbee/fix-tests-with-autocrlf-input-on-windows

Control for core.autocrlf during testing
Rename function to __ prefix
Allow empty config object and use it

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.
Merge pull request #1382 from arrbee/fix-diff-patch-a-different-way

Allow empty config object and use it for tests
Updates to CONTRIBUTING and CONVENTIONS

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.
Simplify diff example using revparse

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!
Fixed a couple typos
Merge pull request #1386 from arrbee/update-docs

Update contributing and conventions
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.
Merge pull request #1387 from carlosmn/kill-indexer

indexer: kill git_indexer
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.
Merge pull request #1388 from carlosmn/hash-ref-delta

indexer: use a hashtable for keeping track of offsets
Fix a few leaks

`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.