If a file entry has the same timestamp as the index itself, it is
considered racily-clean, as it may have been modified after the index
was written, but during the same second. We take extra steps to check
the contents, but this is just one part of avoiding races.

For files which do have changes but have not been updated in the index,
updating the on-disk index means updating its timestamp, which means we
would no longer recognise these entries as racy and we would trust the
timestamp to tell us whether they have changed.

In order to work around this, git zeroes out the file-size field in
entries with the same timestamp as the index in order to force the next
diff to check the contents. Do so in libgit2 as well.

We update the index and then immediately change the contents of the
file. This makes the diff think there are no changes, as the timestamp
of the file agrees with the cached data. This is however a bug, as the
file has obviously changed contents.

The test is a bit fragile, as it assumes that the index writing and the
following modification of the file happen in the same second, but it's
enough to show the issue.

Fix visibility of transaction symbol

path: remove unnecessary readdir_r usage

Arguably all uses of readdir_r are unnecessary, but in this case
especially so, as the directory handle only exists within this function,
so we don't race with anybody.

clone: fall back to copying when linking does not work

Fix in stransport_stream.c for usage of SecCopyErrorMessageString(), which is unavailable to iOS targets.

Binary diffs: store deltas in the diff structure, include binary data in diff callbacks

Fix leaks in tests/checkout/icase

Fix memory leak on windows in diriter.

Transaction.c did not include the visibility definition of its symbol
(that are in git2/transaction.h) and so was by default hidden.

Introduce a new binary diff callback to provide the actual binary
delta contents to callers.  Create this data from the diff contents
(instead of directly from the ODB) to support binary diffs including
the workdir, not just things coming out of the ODB.

Fixed some Secure Transport issues on OS X

travis: fail if we fail the push tests

We need to pass these options in order to have the credentials callback
set.

These tests were not being taken into consideration for the failure of
the test. They've been failing for a while now, but we hadn't noticed as
Travis was reporting the builds successful.

The read and write callbacks passed to SSLSetIOFuncs() have been
rewritten to match the implementation used on opensource.apple.com and
other open source projects like VLC.

This change also fixes a bug where the read callback could get into
an infinite loop when 0 bytes were read.

cred_helpers: Add 'const' qualifiers to git_cred_userpass_payload

Introduce `git_filter_list_contains`

Correct line endings on winhttp.def

indexer: use lseek to extend the packfile

Fixed handling of GIT_DELTA_CONFLICTED  in git_diff_find_similar()

`git_filter_list_contains` can be used to query a filter list to
determine if a given filter will be run.

gitattributes: let clients use native line endings

git_diff_find_similar() now ignores git_diff_delta records with a status
of GIT_DELTA_CONFLICTED, which fixes a crash due to assert() being hit.

Use "text=auto" to ensure that we get LFs in the repository, but
let clients have their native line endings in their worktree.

A few more fixes from coverity

When we hit an error writing to the next stream from a file, we jump to
'done' which currently skips over closing the file descriptor.

Make sure to close the descriptor if it has been set to a valid value.

We take in a possibly partial ID by taking a length and working off of
that to figure out whether to just look up the object or ask the
backends for a prefix lookup.

Unfortunately we've been checking the size against `GIT_OID_HEXSZ` which
is the size of a *string* containing a full ID, whereas we need to check
against the size we can have when it's a 20-byte array.

Change the checks and comment to use `GIT_OID_RAWSZ` which is the
correct size of a git_oid to have when full.

The way we currently do it depends on the subtlety of strlen vs sizeof
and the fact that .pack is one longer than .idx. Let's use a git_buf so
we can express the manipulation we want much more clearly.

`merge_diff_list_count_candidates()` takes pointers to the source and
target counts, but when it comes time to increase them, we're increasing
the pointer, rather than the value it's pointing to.

Dereference the value to increase.

Rather minimal change, but it's the kind of thing we should do.