indexer: move the temporary buffers into the indexer object

Fix mwindow mutex initialization and error checking

This could also use PTHREAD_MUTEX_INITIALIZER, but a dynamic initializer seems like a more portable concept, and we won't need another #define on top of git_mutex_init()

Storing 4kB or 8kB in the stack is not very gentle. As this part has
to be linear, put the buffer into the indexer object so we allocate it
once in the heap.

Indexer speedup with large objects

tree: relax the filemode parser

There are many different broken filemodes in the wild so we need to
protect against them and give something useful up the chain. Don't
fail when reading a tree from the ODB but normalize the mode as best
we can.

As 664 is no longer a mode that we consider to be valid and gets
normalized to 644, we can stop accepting it in the treebuilder. The
library won't expose it to the user, so any invalid modes are a bug.

Fix diff header comments and missing const

Based on the recent work to wrap diff in objective-git, this
includes a fix for a missing const and a number of clarifications
of the documentation.

Version info for public structs

Hey that's not an int!

status should ignore conflicts entries in the index

odb-pack: resurrect pack_backend__read_header

EINVALIDSPEC

To paraphrase @peff:

You can get both size and type from a packed object reasonably cheaply.
If you have:

* An object that is not a delta; both type and size are available in the
  packfile header.
* An object that is a delta. The packfile type will be OBJ_*_DELTA, and
  you have to resolve back to the base to find the real type. That means
  potentially a lot of packfile index lookups, but each one is
  relatively cheap. For the size, you inflate the first few bytes of the
  delta, whose header will tell you the resulting size of applying the
  delta to the base.

For simplicity, we just decompress the whole delta for now.