Hello Mark,
 I like to have Olegh comments, as he has better experiences in using TW 
for scientific contents. But I think


   - A tiddler should have its own numbering starting from 1
   - When we make a big tiddler by transcluding small tiddlers, the macro 
   should take care of correct numbering starting from 1 (this is what you 
   said. the first appeared is first)
   - If a reference deleted in a text, the tiddler should be dynamically 
   update the numbers


BTW, I would like to thank you for your work. I think what you did e.g. 
each reference has a tiddler is a great idea! This give us huge 
flexibility. The only problem is here the wiki soon get crowded with 
reference tiddlers.

- Mohammad

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