Rewrite AtomicDirectory.

The previous version didn't close its FDs for directories, and called
fsync() on the wrong FDs. To make sure a rename() is persisted, we
need to call fsync() on the FD of the parent directory, because file
names are stored in directory entries instead of inodes.

Also removed the need for dedicated native code by calling the Os
class directly.

Fixes: 139302541
Bug: 138866253
Test: presubmit
Change-Id: I67fe98811814acba5158d760766a2ef3b121225a