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.)
Disable ignore_case when writing the index to a tree
Rename function to __ prefix
clear REUC on checkout
Merge pull request #1390 from ethomson/reuc_clear

clear REUC on checkout
Merge pull request #1380 from phkelley/index_icase

Disable ignore_case when writing the index to a tree
Make sure docurium can see git_packbuilder_foreach
Merge pull request #1369 from arrbee/repo-init-template-hooks

More tests (and fixes) for initializing repo from template
remote push test fix
Merge pull request #1392 from ethomson/push_test_fix

remote push test fix
basic note iterator implementation

* git_note_iterator_new() - create a new note iterator
* git_note_next() - retrieves the next item of the iterator
use git_note_iterator type instead of non-public git_iterator one
MSVC: Define NDEBUG to disable asserts in release builds
fixed minor issues with new note iterator

* fixed style issues
* use new iterator functions for git_note_foreach()
added missing free for git_note in clar tests
Merge pull request #1396 from cholin/features/note-iterator

[RFC] basic note iterator implementation
No longer need clar_main.c
Notify '*' pathspec correctly when diffing

I also moved all tests related to notifying in their own file.