You can try md_docer.py plugin. I remember writing it for someone with similar 
problem. Using it you can define one or more transformer scripts with the 
headline like "@transformer mytransformer". This script has access to g, c, p 
and out vars. Out is a file like object. Script should write its output to out. 
Nodes with the headline like " @transform-node mytransformer(somegnx)" will 
have the output of transformation mytansformer of node with the given somegnx.

Transformations can be executed as minibuffer command or by default on every 
save.

HTH Vitalije

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