Change tree-id config to specify a file with the tree-id in.

Replaces tree-id config option with tree-id-file, where the new option names a file where the id is stored.

For consistency, rename a few other options (without any change in meaning): rate-limit-config --> rate-limit-config-file, secondary-pub-key --> secondary-pub-key-file, sth-path --> sth-file. Corresponding command line flags also renamed for consistency.