USE_NSECS fixes

Coverity fixes

Extra checks for packfile indices

Android NDK does not have a `struct timespec` in its `struct stat`
for nanosecond support, instead it has a single nanosecond member inside
the struct stat itself.  We will use that and use a macro to expand to
the `st_mtim` / `st_mtimespec` definition on other systems (much like
the existing `st_mtime` backcompat definition).

The index::nsec::staging_maintains_other_nanos test was created to
ensure that when we stage an entry when GIT_USE_NSECS is *unset* that
we truncate the index entry and do not persist the (old, invalid)
nanosec values.  Ensure that when GIT_USE_NSECS is *set* that we do
not do that, and actually write the correct nanosecond values.

A corrupt index might have data that tells us to go look past the end of
the file for data. Catch these cases and return an appropriate error
message.

CONVENTIONS: update to include general public API principles

This got lost duing the move and it lets the users call this function
just in case.

Minor `giterr` fixups

The `giterr_set_str` does not actually honor `GITERR_OS`.  Remove
the documentation that claims that we do.

Use the `giterr_set` function, which actually supports `GITERR_OS`.
The `giterr_set_str` function is exposed for external users and will
not append the operating system's error message.

The `normalize_find_opts` function in theory allows for the
incoming diff to have no repository. When the caller does not
pass in diff find options or if the GIT_DIFF_FIND_BY_CONFIG value
is set, though, we try to derive the configuration from the
diff's repository configuration without first verifying that the
repository is actually set to a non-NULL value.

Fix this issue by explicitly checking if the repository is set
and if it is not, fall back to a default value of
GIT_DIFF_FIND_RENAMES.

Convert `rebase_alloc` to use our usual error propagation
patterns, that is accept an out-parameter and return an error
code that is to be checked by the caller. This allows us to use
the GITERR_CHECK_ALLOC macro, which helps static analysis.

Set the error code when an error occurs in any of the called
functions. This ensures we pass the error up to callers and
actually free the remote when an error occurs.

The overflow check in `read_reuc` tries to verify if the
`git__strtol32` parses an integer bigger than UINT_MAX. The `tmp`
variable is casted to an unsigned int for this and then checked
for being greater than UINT_MAX, which obviously can never be
true.

Fix this by instead fixing the `mode` field's size in `struct
git_index_reuc_entry` to `uint32_t`. We can now parse the int
with `git__strtol64`, which can never return a value bigger than
`UINT32_MAX`, and additionally checking if the returned value is
smaller than zero.

We do not need to handle overflows explicitly here, as
`git__strtol64` returns an error when the returned value would
overflow.

The fail-label of `reflog_parse` explicitly checks the entry
poitner for NULL before freeing it. When we jump to the label the
variable has to be set to a non-NULL and valid pointer though: if
the allocation fails we immediately return with an error code and
if the loop was not entered we return with a success code,
withouth executing the label's code.

Remove the useless NULL-check to silence Coverity.

When invoking `diff_print_info_init_frompatch` it is obvious that
the patch should be non-NULL. We explicitly check if the variable
is set and continue afterwards, happily dereferencing the
potential NULL-pointer.

Fix this by instead asserting that patch is set. This also
silences Coverity.

The function `compute_write_order` may return a `NULL`-pointer
when an error occurs. In such cases we jump to the `done`-label
where we try to clean up allocated memory. Unfortunately we try
to deallocate the `write_order` array, though, which may be NULL
here.

Fix this error by returning early instead of jumping to the
`done` label. There is no data to be cleaned up anyway.

When no payload is set for `crlf_apply` we try to compute the
crlf attributes ourselves with `crlf_check`. When the function
determines that the current file does not require any treatment
we return the GIT_PASSTHROUGH error code without actually
allocating the out-pointer, which indicates the file should not
be passed through the filter.

The `crlf_apply` function explicitly checks for the
GIT_PASSTHROUGH return code and ignores it. This means we will
try to apply the crlf-filter to the current file, leading us to
dereference the unallocated payload-pointer.

Fix this obviously incorrect behavior by not treating
GIT_PASSTHROUGH in any special way. This is the correct thing to
do anyway, as the code indicates that the file should not be
passed through the filter.

We commonly have to check if a git_buf has been allocated
correctly or if we ran out of memory. Introduce a new macro
similar to `GITERR_CHECK_ALLOC` which checks if we ran OOM and if
so returns an error. Provide a `#nodef` for Coverity to mark the
error case as an abort path.

Coverity does not comprehend the connection between a vector's
size and the contents pointer, that is that the vector's pointer
is non-NULL when its size is positive. As the vector code should
be reasonably well tested and users are expected to not manually
modify a vector's contents it seems save to assume that the
macros will never dereference a NULL pointer.

Fix Coverity warnings by overriding the foreach macros with
macros that explicitly aborting when (v)->contents is NULL.

git_libgit2_opts: minor documentation & usage fixes

Fix a few checkout -> rebase typos

We need to include the header where we define the function. Otherwise it
won't be available on the DLL.