Use checksums to detect config file changes

Fix build for custom transport users

merge-base: Remove redundant merge bases

This reduces the chances of a crash in the thread tests. This shouldn't
affect general usage too much, since the main usage of these functions
are to read into an empty buffer.

Instead of relying on the size and timestamp, which can hide changes
performed in the same second, hash the file content's when we care about
detecting changes.

We currently use the timestamp in order to decide whether a config file
has changed since we last read it.

This scheme falls down if the file is written twice within the same
second, as we fail to detect the file change after the first read in
that second.

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