You can clone with
I did a quick search and didn't find this mentioned anywhere. I happened to run across this thread over on the WP support forums where a theme and plugin have both used this library and it results in both trying to declare the same functions.
Is this a case of them not doing something right? Is there a recommended way of including this in multiple plugins and avoiding clashes like this?
Yes, if you follow the model in example-functions.php (and change the cmb_sample_metaboxes function to a properly prefixed function), It should automatically avoid conflicts. That is what the class_exists( 'cmb_Meta_Box' ) check is for. However, there's no guarantees that all plugins/themes are doing those two steps.
class_exists( 'cmb_Meta_Box' )