This allows us to remove OS checks from source code, instead relying
on CMake to detect whether or not `struct stat` has the nanoseconds
members we rely on.
As we attempt to replicate a situation in which an older checkout has
put a file on disk with different filtering settings from us, set the
timestamp on the entry and file to a second before we're performing the
operation so the entry in the index counts as old.
This way we can test that we're not looking at the on-disk file when the
index has the entry and we detect it as clean.
The signature for the reflog is not something which changes
dynamically. Almost all uses will be NULL, since we want for the
repository's default identity to be used, making it noise.
In order to allow for changing the identity, we instead provide
git_repository_set_ident() and git_repository_ident() which allow a user
to override the choice of signature.
git_checkout_index can now check out other git_index's (that are not
necessarily the repository index). This allows checkout_index to use
the repository's index for stat cache information instead of the index
data being checked out. git_merge and friends now check out their
indexes directly instead of trying to blend it into the running index.
