Move system directory cache out of utils

Include stdarg.h for the va_copy test

Fix Intel compiler warnings

Improve documentation for merging

Check if librt exists independent of OS, to be able to exclude librt on ...

Improve C89 compatibility and clarify use of C99 features

Check if librt exists independent of OS, to be able to exclude librt on Android builds, even though it is a 'Linux'.

* Make GIT_INLINE an internal definition so it cannot be used in
  public headers
* Fix language in CONTRIBUTING
* Make index caps API use signed instead of unsigned values

and a couple of other minor doc fixups.

Improve error propagation in shallow call

Check for EWOULDBLOCK as well as EAGAIN on write.

On some systems, notably HP PA-RISC systems running Linux or HP-UX,
EWOULDBLOCK and EAGAIN are not the same value.  POSIX (and these OSes) allow
EWOULDBLOCK to occur on write(2) (and send(2), etc.), so check explicitly
for this case as well as EAGAIN by defining and using a macro GIT_ISBLOCKED
that considers both.

The macro is necessary because MSYS does not provide EWOULDBLOCK and
compilation fails if an attempt is made to use it unconditionally.  On most
systems, where the two values are the same, the compiler will simply
optimize this check out and it will have no effect.

Fix filter test for CRLF->LF issues

Never convert CRLF->LF

Core git performs no conversion on systems that use LF, emulate that.

Handle `core.autocrlf=input` when checking out

Conditional ref update fixups

Keep the reflog parameters as the last two, as they're the optional
parameters.

This addresses arrbee's concerns about wording in the conditional
reference udpate functions.

Not closing the files on a diff failure ensures that clar
cleanup will fail on win32 because we still have the file open.

 add example for diff with --numstat

Add git_commit_amend API