Cast actual filesystem data to the int32_t that index entries store.

index: preserve extension parsing errors

Ensure that we do not use any deprecated functions in the library
source, test code or examples.

Move the deprecated stream tests into their own compilation unit.  This
will allow us to disable any preprocessor directives that apply to
deprecation just for these tests (eg, disabling `GIT_DEPRECATED_HARD`).

Previously, we would clobber any extension-specific error message with
an "extension is truncated" message. This makes `read_extension`
correctly preserve those errors, takes responsibility for truncation
errors, and adds a new message with the actual extension signature for
unsupported mandatory extensions.

Move to the `git_error` name in the internal API for error-related
functions.

In include/git2/odb.h it states that callback can also return
positive value which should break looping.

Implementations of git_odb_foreach() and pack_backend__foreach()
did not respect that.

Move `git_ref_t` to `git_reference_t`

More `git_obj` to `git_object` updates