Add option to ignore file mode in diffs

Diff API signatures

A number of diff APIs and the `git_checkout_index` API take a
`git_repository` object an operate on the index.  This updates
them to take a `git_index` pointer explicitly and only fall back
on the `git_repository` index if the index input is NULL.  This
makes it easier to operate on a temporary index.

The index iterator could previously only be created from a repo
object, but this allows creating an iterator from a `git_index`
object instead (while keeping, though renaming, the old function).

The diff API is not in the parameter order one would expect from
other libgit2 APIs.  This fixes that.

Explain a few CMake options in the README

Expose STDCALL and explain a few useful CMake options, as well as
explain the quirks building on Windows.

Allocate with calloc rather than conditionally memsetting a specific
part of the struct later on.

Deal with empty and nonexsitent values in config

Returning NULL for the string when we haven't signaled an error
condition is counter-intuitive and causes unnecessary edge
cases. Return an empty string when asking for a string value for a
configuration variable such as '[section] var' to avoid these edge
cases.

If the distinction between no value and an empty value is needed, this
can be retrieved from the entry directly. As a side-effect, this
change stops the int parsing functions from segfaulting on such a
variable.

Update checkout with new strategies & behavior

'[section] variable' and '[section] variable =' behave differently
when parsed as booleans, so we need to store that distinction
internally.

We're already in the git_config namespace, there is no need to repeat
it.

Win32 CryptoAPI and CNG support for SHA1

Bump the builtin http-parser to v2.0

Fix memory leaks

repository: Refine repository_head() error report

The indexer handles this better than the fetch
logic does.

create FETCH_HEAD specially instead of as a ref file

Duplicate tree entries