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.

Remove sample hook files

Getting rid of sample hook files from test repos as they just take up
space with no value.

Portability fixes for Solaris

Do not fail if .gitignore is directory

This is designed to fix libgit2sharp #350 where if .gitignore is
a directory we abort all operations that process ignores instead
of just skipping it as core git does.

Also added test that fails without this change and passes with it.

Teach git_branch_remote_name() to work with orphaned heads

Fix git_stash_drop()

add a sorter to the reuc on index creation

Add more treebuilder tests

The recent changes with git_treebuilder_entrycount point out that
the test coverage for git_treebuilder_remove and
git_treebuilder_entrycount is completely absent.  This adds tests.

Add explicit entrycount to tree builder

This replaces most of the explicit vector iteration with calls
to git_vector_foreach, adds in some git__free and giterr_clear
calls to clean up during some error paths, and a couple of
other code simplifications.

The treebuilder entries vector flags removed items which means
we can't rely on the entries vector length to accurately get the
number of entries.  This adds an entrycount value and maintains it
while updating the treebuilder entries.

Simplify signature parsing

Disable caching in Clar

Fix static analyzer issues

The cppcheck static analyzer generates warnings for a bunch of
places in the libgit2 code base.  All the ones fixed in this
commit are actually false positives, but I've reorganized the
code to hopefully make it easier for static analysis tools to
correctly understand the structure.  I wouldn't do this if I
felt like it was making the code harder to read or worse for
humans, but in this case, these fixes don't seem too bad and will
hopefully make it easier for better analysis tools to get at any
real issues.

If gethostbyname() fails on platforms with NO_ADDRINFO, the code
leaks the struct addrinfo that was allocated.  This fixes that
(and a number of code formatting issues in that area of code in
src/posix.c).

There were a number of functions assigning their return value to
`error` without much explanation.  I added in some rudimentary
error checking to help flesh out the example.

Also, I reformatted all of the comments down to 80 cols (and in
some cases, slightly updated the wording).

push: fix typo in git_push_finish() doc

Topic/diff tree coverage

push: improve docs on success / failure of git_push_finish