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.

This reverts commit efe7fad6, except for
the indentation fixes.

hash: remove git_hash_init from internal api

Along with that, fix indentation in tests-clar/object/raw/hash.c

Initialize the hash ctx with git_hash_ctx_init, not git_hash_init.

packbuilder: minor improvements

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.