It's been a few years since I've played with it, but Leo[1] seems like it might be what the author is looking for. It's even scriptable (in Python). Looks like it is actively maintained[2].
I was just about to write that...
I barely know it but it seems it can be summed up as a hybrid of mind mapping [1] and literate programming [2], with a graph data model [3].
It's status somewhat resembles Org Mode: it has its own format (which hasn't caught on as interchange format) but has sufficient manipulation and export power to allow some people to spend their life inside it.
---
The second thing that spings to mind is YAML which is usually used for trees but the actual data model allows graphs.
Is there any structured YAML editor (a-la paredit)?
http://leoeditor.com/
https://github.com/leo-editor/leo-editor