runtime: Ensure container gets cleaned up on shutdown

Recent refactoring to simplify the Runtime class inadvertantly removed
the cleanup code. As a result, a container would not be stopped and
removed when shrinkwrap exits but would linger, using system resources.

Fix that by reintroducing the cleanup code.

Fixes: 1db05f5a ("runtime: replace modal stack with singleton")
Signed-off-by: Ryan Roberts <ryan.roberts@arm.com>