Hi
I guess this is something some (many?) of us are looking for... and haven't found as yet. I'm just a lecturer and researcher who does quite a lot of academic writing, and a Mac user. So I might not get the technical aspects. These are some thoughts onn the matter.
I use DEVONThink Pro to sort and organize most of my research stuff. I'm looking forward to version 2 so it will handle properly Word and other docs, it will keep all files in the Finder and allow for a easy use of tags/keywords.
I use Bookends as my bibliography reference manager, although I try to keep pdfs in DT Pro.
I use Scrivener to draft texts, which I then "layout" and polish them in Word or Mellel (I like the latter a lot, but I have to share docs with people that use Word). Other people do that in Pages or NisusWriter Pro. It's similar to the workflow described here:
http://homepage.mac.com/kvmagruder/hsci ... kflow.html by Kerry Magruder some time ago.
Each of these apps has great things, and room for improvement too. IdeaMason (which I only know from the tutorials on it's website) has some nice ideas for that.
But the need for some kind of integrated environment à la IdeaMason is still there. I guess that could be achieved (if it ever is) either by porting IdeaMason to the Mac/developing a new app from scratch, or by better integrating apps like DT, BE and Scriv.
It would be great to select a file in DT Pro and click a button to create a new record in Bookends, attach the file to the new record without moving it, have it try to autocomplete the data and let you do it if DT cannot. It would be great if you could drag a DTPro group or folder (a smart one even better) to Scrivener's Research sidebar folder and view the contents directly there. More or less the way Apple apps may access iLife's photos, video and audio "assests". And of course some interface "harmonisation" would help.
I'd let out the final retouching for Word/Mellel/Pages/Nisus or whatever. For that the main thing would be to be able to set some basic text structure in Scrivener or DT's word processor (which I believe is Apple's Text Engine), that is, headings 1 to 6, lists, footnotes, etc. and have them understood properly by Word/Mellel/Pages. From several posts in DT, Mellel, Scrivener and other forums, I collect the main bottleneck is in Apple's Text Engine and the use of rtf.
It be interesting if someone with better technical knowledge could elaborate on these ideas, to tell us if they are feasible or not, difficult or not, likely or not. (Well, likely is not exactly a technical question

)
Any other ideas?
Regards
Manuel Aguilar Hendrickson