Following on from @zmk's suggestion in #41, I do like the idea of having an XML file as a configuration for registering plugins and options - the structure is such that it would be relatively trivial to understand, and read from.
Without restricting where the plugin and configuration should go (together) within a theme, looking for a tgmpa.xml file in the same directory as the class file (or thinking of a way to pass in a reference to the class file), or one level above it if it doesn't exist may work sufficiently well.
Update: A JSON config file should also be considered.
Why not JSON instead?
JSON may well be the better lightweight storage method here - I tend to just think of config files as more easily readable in <...> blocks than JSON brackets, quotes, semi-colons et al.
XML configuration files were invented because you can't define associative arrays directly in Java. There's no need for them in any modern, interpreted programming language.