Fix build for custom transport users

merge-base: Remove redundant merge bases

index: read_index must update hashes

We should explicitly include the declaration of git_strarray
from "include/git2/sys/transport.h"

Fix segfault when reading reflog with extra newlines

Using calloc instead of malloc because the parse error will lead to an immediate free of committer (and its properties, which can segfault on free if undefined - test_refs_reflog_reflog__reading_a_reflog_with_invalid_format_returns_error segfaulted before the fix).

#3458

pool: Simplify implementation

cc @carlosmn

Better REUC generation when merging

Inserting new REUC entries can quickly become pathological given that
each insert unsorts the REUC vector, and both subsequent lookups *and*
insertions will require sorting it again before being successful.

To avoid this, we're switching to `git_vector_insert_sorted`: this keeps
the REUC vector constantly sorted and lets us use the `on_dup` callback
to skip an extra binary search on each insertion.

Fix docs typo geterr_clear -> giterr_clear

inttypes.h is built-in header file since MSVC 2013

cmake: split sources into original paths for Xcode and MSVC

xdiff: reference util.h in parent directory

merge: add GIT_MERGE_TREE_FAIL_ON_CONFLICT

The MSVC_SPLIT_SOURCES function is helpful for other IDEs, like Xcode,
and will split the source files up into their target directories,
instead of merely placing them all in a "Sources" directory.

Rename MSVC_SPLIT_SOURCES to IDE_SPLIT_SOURCES and enable it for Xcode.

Provide a new merge option, GIT_MERGE_TREE_FAIL_ON_CONFLICT, which
will stop on the first conflict and fail the merge operation with
GIT_EMERGECONFLICT.

Nanoseconds in the index: ignore for diffing

Although CMake will correctly configure include directories for us,
some people may use their own build system, and we should reference
`util.h` based on where it actually lives.

Although our index contains the literal time present in the index,
we do not read nanoseconds from disk, and thus we should not use
them in any comparisons, lest we always think our working directory
is dirty.

Guard this behind a `GIT_USE_NSECS` for future improvement.

Test that nanoseconds are round-tripped correctly when we read
an index file that contains them.  We should, however, ignore them
because we don't understand them, and any new entries in the index
should contain a `0` nsecs field, while existing preserving entries.

The reason is that the types defined in libgit2's inttypes.h collide with system inttypes.h
3rd party library header files may directly reference MSVC's built-in inttypes.h

Fixes #3476