Don't go to the ODB to resolve zero byte files in the workdir

Preserve tree filemode in index during checkout

Don't try to determine whether the system supports file modes
when putting the tree data in the index during checkout.  The tree's
mode is canonical and did not come from stat(2) in the first place.

Expose patch serialization to git_buf

It's hard or even impossible to correctly free the string buffer
allocated by git_patch_to_str in some circumstances. Drop the function
so people have to use git_patch_to_buf instead - git_buf has a dedicated
destructor.

Returning library-allocated strings from libgit2 works fine on Linux,
but may cause problems on Windows because there is no one C Runtime that
everything links against. With libgit2 not exposing its own allocator,
freeing the string is a gamble.

git_patch_to_str already serializes to a buffer, then returns the
underlying memory. Expose the functionality directly, so callers can use
the git_buf_free function to free the memory later.

Merge improvements

The "merge none" (don't automerge) flag was only to aide in
merge trivial tests.  We can easily determine whether merge
trivial resulted in a trivial merge or an automerge by examining
the REUC after automerge has completed.

The default merge_file level was XDL_MERGE_MINIMAL, which will
produce conflicts where there should not be in the case where
both sides were changed identically.  Change the defaults to be
more aggressive (XDL_MERGE_ZEALOUS) which will more aggressively
compress non-conflicts.  This matches git.git's defaults.

Increase testing around reverting a previously reverted commit to
illustrate this problem.

"Uninitialized" submodules are "unmodified"

Extend the "unmodified" submodule workdir test to include
uninitialized submodules, to prevent reporting submodules as
modified when they're not in the workdir at all.

git_reflog_entry_message can be null

Fix a couple of corner cases and an undefined behavior

Fix segfault when calling git_config_get_* functions when a config fails to load

Reinitialize the result code of get_entry() to GIT_ENOTFOUND

Convert gitdir paths to posix on Windows

Apparently, a .git file with "gitdir: path" link on Windows is
allowed to use backslashes in the path.  Who knew?

Fix some documentation issues.

Run Coverity scan on Travis

Update README to include Java, PowerShell bindings

refs: remove the _with_log differentiation

Any well-behaved program should write a descriptive message to the
reflog whenever it updates a reference. Let's make this more prominent
by removing the version without the reflog parameters.

Common

Align `*_dup` functions

Implement @cmn's suggestions for `git_remote_dup`.