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

This reverts commit 8c535f3f.

Older versions of git would only write peeled entries for
items under refs/tags/. Newer versions will write them for
all refs, and we should be prepared to handle that.

More packfile locking

There is an occasional assertion failure in sha1_entry_pos from
pack_entry_find_index when running threaded.  Holding the mutex
around the code that grabs the index_map data and processes it
makes this assertion failure go away.

We need to hammer the packfile open phase harder in the thread
tests, in addition to the cache API.

We were still seeing a few issues in threaded access to packs.
This adds extra locks around the opening of the mwindow to
avoid a different race.

allow empty dirs to exist when doing checkout

Merge trees

Namespace support

Update diff handling of "untracked" directories

This includes more tests for various scenarios when diff includes
an untracked directory in the workdir with contents either ignored
or not.

When diff encounters an untracked directory, there was a shortcut
that it took which is not compatible with core git.  This makes
the default behavior no longer take that shortcut and instead look
inside the untracked directory to see if there are any untracked
files within it.  If there are not, then the directory is treated
as an ignore directory instead of an untracked directory.  This
has implications for the git_status APIs.

In preparation for more changes to the internal diff logic, it
seemed wise to split the very large git_diff__from_iterators into
separate functions that handle the four main cases (unmatched old
item, unmatched new item, unmatched new directory, and matched
old and new items).  Hopefully this will keep the logic easier to
follow even as more cases have to be added to this code.

Remove most inlines from the public API

Add refspec list accessors

Catch issue in config set with no config file

This prevents a segfault when setting a value in the config of a
repository that doesn't have a config file.

Bring back a way of acessing the git_refspec* from a remote.

Closes #1514