Diff patch bug fixes

When a patch contained an eofnl change (i.e. the last line either
gained or lost a newline), the oldno and newno line number values
for the lines in the last hunk of the patch were not useful.  This
makes them behave in a more expected manner.

This adds a new line origin constant for the special line that
is used when both files end without a newline.

In the course of writing the tests for this, I was having problems
with modifying a file but not having diff notice because it was
the same size and modified less than one second from the start of
the test, so I decided to start working on nanosecond timestamp
support.  This commit doesn't contain the nanosecond support, but
it contains the reorganization of maybe_modified and the hooks so
that if the nanosecond data were being read by stat() (or rather
being copied by git_index_entry__init_from_stat), then the nsec
would be taken into account.

This new stuff could probably use some more tests, although there
is some amount of it here.

fix git_branch_set_upstream for local branches

Fixed qsort_r() problem when targeting AmigaOS.

We fall back to the libgit2-provided insert sort as done for other
platforms.

Add git_commit_owner to the public interface

Just like git_tree_owner, etc.

Currently git_branch_set_upstream when passed a local branch
creates invalid configuration, for ex. if we setup branch
'tracking_master' to track local 'master' libgit2 generates
the following config

```
[branch "track_master"]
  remote = .
  merge = .refs/heads/track_master
```

The merge value is invalid and calling git_branch_upstream on
'tracking_master' results in invalid reference error.

It should do:

```
[branch "track_master"]
  remote = .
  merge = refs/heads/master
```

p_stat() should follow symlinks on windows

Make sure error messages are set for most error returns

By default do not set tagopt when cloning

allow checkout to proceed when a dir to be removed is in use (win32)

branch.h: fix typo in docs

Strict/lax commit API

Peeling to an invalid type is now checked via an assert so this
test is no longer relevant.

fix some leaks

braces

puns are not funny; type punning especially so

Switch to index_version as "git_pack_file is ready" flag

We use p->index_map.data to check whether the struct has been set up
and all the information about the index is stored there. This variable
gets set up halfway through the setup process, however, and a thread
can come along and use fields that haven't been written to yet.

Crucially, pack_entry_find_offset() needs to read the index version
(which is written after index_map) to know the offset and stride
length to pass to sha1_entry_pos(). If these values are wrong,
assertions in it will fail, as it will be reading bogus data.

Make index_version the last field to be written and switch from using
p->index_map.data to p->index_version as "git_pack_file is ready" flag
as we can use it to know if every field has been written.

refdb_fs: do not require peeled packed refs to be tags

We only set our negative flag for PEELING_FULL; we can fall
back to the lesser PEELING_STANDARD if our ref is in the
refs/tags/ hierarchy.

This makes parsing easier! :p

Fixes #1532