Direct mode is great because it removes symlinks. A must-have for directories like `~/Documents`. Unfortunately, it removes the possibility to use `git` commands other than `git-annex`. Also, it doen't preserve history of files.

I would be great to have a mode where:

- files are available in plain, not as sylinks
- the repository could still be trusted to hold version of some files from other repositories
- from a user point of view, the history of a file before the checkout would be preserved.

In feature rich file systems that have copy on write feature, it could be implemented by having the files in both places at the same time:

- the current version of a file would be in the working copy
- the file in the working copy would be a copy-on-write of the file in the annex repository
- when the file in the working copy changes, `git-annex` notices it and copy the file in the annex repository using copy-on-write semantic

If the file system do not support copy-on-write, it could be an option (do you want secure direct mode that takes twice the disk space or light direct mode that don't preserve the history of your files?)

This would make direct more much more robust.

copy on write is available using `cp --reflink=always`. It correspond to the following code ([coreutils src/copy.c line 224](http://git.savannah.gnu.org/cgit/coreutils.git/tree/src/copy.c#n224)):

    /* Perform the O(1) btrfs clone operation, if possible.
       Upon success, return 0.  Otherwise, return -1 and set errno.  */
    static inline int
    clone_file (int dest_fd, int src_fd)
    {
    #ifdef __linux__
    # undef BTRFS_IOCTL_MAGIC
    # define BTRFS_IOCTL_MAGIC 0x94
    # undef BTRFS_IOC_CLONE
    # define BTRFS_IOC_CLONE _IOW (BTRFS_IOCTL_MAGIC, 9, int)
      return ioctl (dest_fd, BTRFS_IOC_CLONE, src_fd);
    #else
      (void) dest_fd;
      (void) src_fd;
      errno = ENOTSUP;
      return -1;
    #endif
    }

Looking at the code it would be preferable to exec directly to `cp`, see [copy_range() on LWN](http://lwn.net/Articles/550621/) and this [more recent article about splice() on LWN](http://lwn.net/Articles/567086/)

Also, `cp --reflink` fall back to copy when copy-on-write is not available while `cp --reflink=always` do not.