[Native File System] Correctly refcount isolated file systems.

Uses the handles IsolatedContext returns in the Native File System
implementation to keep the isolated FS alive appropriately.

Bug: 955185
Change-Id: I7c12a3ed02a083c078b4aaf9bfbe355b0407e38a
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/1601976
Commit-Queue: Marijn Kruisselbrink <mek@chromium.org>
Reviewed-by: Victor Costan <pwnall@chromium.org>
Cr-Commit-Position: refs/heads/master@{#661935}