Apply filters when writing index

There is no "z" size specifier on MSVC

See http://msdn.microsoft.com/en-us/library/tcxf1dw6.aspx and https://stackoverflow.com/questions/6655410/why-doesnt-zd-printf-format-work-in-vs2010

Signed-off-by: Sven Strickroth <email@cs-ware.de>

Minor cleanups for master

If there is a failure then cl_git_pass tries to get the libgit2
error, but p_... functions don't set that.

Also - trailing whitespace cleanup.

FLAG_BITS only seems to be used internally

Fill the tree cache when reading in a tree into an index

An obvious place to fill the tree cache is on write-tree, as we're
guaranteed to be able to fill in the whole tree cache.

The way this commit does this is not the most efficient, as we read the
root tree from the odb instead of filling in the cache as we go along,
but it fills the cache such that successive operations (and persisting
the index to disk) will be able to take advantage of the cache, and it
reuses the code we already have for filling the cache.

Filling in the cache as we create the trees would require some
reallocation of the children vector, which is currently not possible
with out pool implementation. A different data structure would likely
allow us to perform this operation at a later date.

If e.g. the root tree is invalidated, we still want to write out
its children, since those may still have valid cache entries.

Keeping the cache around after read-tree is only one part of the
optimisation opportunities. In order to share the cache between program
instances, we need to write the TREE extension to the index.

Do so, taking the opportunity to rename 'entries' to 'entry_count' to
match the name given in the format description. The included test is
rather trivial, but works as a sanity check.

This wasn't used. We invalidate based on the full path, so we always go
down the tree, never up.

These test that we invalidate at the right levels and that we remove the
tree cache when clearing the index.

When reading from a tree, we know what every tree is going to look like,
so we can fill in the tree cache completely, making use of the index for
modification of trees a lot quicker.

This simplifies freeing the entries quite a bit; though there aren't
that many failure paths right now, introducing filling the cache from a
tree will introduce more. This makes sure not to leak memory on errors.

remote: accept a repository and remote name for deletion

[factor] Join typedef and struct definitions in single file.

Some PRs have fallen out of sync with the changes in signatures, so we
need to take a few extra parameters into account.

Can read large file larger than 2GB on Win64

Fix warnings in thread-utils.h when building without -DTHREADSAFE=ON

Do not error out when fetching from second remote

Provide option to embed libssh2

Add support for setting the SSL CA location

Allow to propagate checkout callbacks to git HARD reset

Provide host name to certificate_check_cb

New test files for the javascript diff driver.

Walk only as far as the common ancestors of uninteresting commits

Treat an empty list of refspecs the same as a NULL value.

Implement git-describe

config: Handle multiple spaces that follow a configuration value and precede a comment char

Fix README.md