Diff and status do not want core.safecrlf to actually raise an error regardless of the setting, so this extends the filter API with an additional options flags parameter and adds a flag so that filters can be applied with GIT_FILTER_OPT_ALLOW_UNSAFE, indicating that unsafe filter application should be downgraded from a failure to a warning.
There were a couple of "init_opts()" functions a few more cases of structure initialization that I somehow missed.
When diff is scanning the working directory, if it finds a file where it is not sure if the index entry matches the working dir, it will recalculate the OID (which is pretty expensive). This adds a new flag to diff so that if the OID calculation finds that the file actually has not changed (i.e. just the modified time was altered or such), then it will refresh the stat cache in the index so that future calls to diff will not have to check the oid again.
This reorganized the diff OID calculation to make it easier to correctly update the stat cache during a diff once the flags to do so are enabled. This includes marking the path of a git_index_entry as const so we can make a "fake" git_index_entry with a "const char *" path and not get warnings. I was a little surprised at how unobtrusive this change was, but I think it's probably a good thing.
In the iterator, distinguish between ignores and empty directories so that diff and status can ignore empty directories, but checkout and stash can treat them as untracked items.
When diff finds an untracked directory, it emulates Git behavior by looking inside the directory to see if there are any untracked items inside it. If there are only ignored items inside the dir, then diff considers it ignored, even if there is no direct ignore rule for it. Checkout was not copying this behavior - when it found an untracked directory, it just treated it as untracked. Unfortunately, when combined with GIT_CHECKOUT_REMOVE_UNTRACKED, this made is seem that checkout (and stash, which uses checkout) was removing ignored items when you had only asked it to remove untracked ones. This commit moves the logic for advancing past an untracked dir while scanning for non-ignored items into an iterator helper fn, and uses that for both diff and checkout.
To emulate git, stash should not remove untracked git repositories inside the parent repo, and checkout's REMOVE_UNTRACKED should also skip over these items. `git stash` actually prints a warning message for these items. That should be possible with a checkout notify callback if you wanted to, although it would require a bit of extra logic as things are at the moment.
Clear up some of the various "find" functions and the snapshot API naming to be things I like more.
Again, laying groundwork for some index iterator changes, this contains a bunch of code refactorings for index internals that should make it easier down the line to add locking around index modifications. Also this removes the redundant prefix_position function and fixes some potential memory leaks.