Custom numbering
I think it would be good if zotero would have 1 more field for custom numbering. With this one can make logical order in the folders. Not just listing by title etc. but listing by custom number.
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http://forums.zotero.org/discussion/33/
http://forums.zotero.org/discussion/694/
But as I say on that other thread, the field already exists in the data layer. It's just a question of actually handling it in all the places it would have to be handled for it to be useful (items list, reports, etc.). And, while you're right that it wouldn't have to be exportable for most of the export formats, I'm pretty sure people would expect the order to be preserved when exporting and importing a collection as Zotero RDF.
What if I'm working on two projects at once? Should I need to go back and manually set the order every single time I want to revisit a collection? There's no reason changing the order of items in one collection should affect the order of items in all others.
I think your basic premise is a little off here. This isn't done with user-entered numbers, and certainly not global ones. You drag items around into the order you want, and that automatically adjusts the order number of the dragged item and all other items in the collection. The order has no effect on other collections. This already happens behind-the-scenes in Zotero, though dragging into an order isn't yet supported.
Take a look at iTunes playlists here for the parallel—it's the exact same idea. The main library has no order field; only playlists do. In playlists, you drag songs around into the order you want, and this automatically adjusts the number field, which you can sort by if you want. If you arrange songs into a particular order in one playlist, it doesn't affect the order in another, so you can always return to a playlist and burn the same CD.
This I did not know :D
The scene what you have described would be absolutely perfect for me (although I do not have an iPod and I'm not using iTunes, i think I've understood what you've meant) The same what I was thinking of, just I thought it would be easier to give custom numbers. I really like the idea to handle the collections like playlist athough I do not know if I change the listing to alphabetical order how can it be changed back to a custom order...
As for conflicts when merging databases, I have to agree with Con_Sole. Entries with the same author get sorted by a secondary field (i.e. date or paper title), so entries with the same custom field can be treated the same. If I found that I had two entries with the same custom field after a merge, then I would just change one to keep my 'system' intact. Hence the beauty of 'custom' fields.
Note: By system I mean that I keep a folder of PDF files on my flashdrive so that I can access them as needed without loading firefox and zotero. I number these PDFs incrementally as I collect them, so I can find them easily later. I would love this number to be linked to zotero somehow.