I suppose
I suppose it is way to late to ask if zotero could be programmed to use multiple containers, each a separate library able to be linked to a separate database so that we can load up different projects without having them become mingled together into one. This would also solve the problem of keeping the shared project database separate from personal files.
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http://support.mozilla.com/en-US/kb/Managing+profiles
Bruce has the better advice; there is something wrong with my suggestion to run separate Firefox profiles, actually. If you have Firefox 1 and Firefox 2, say, each will have a completely separate database. If you write a document using Firefox 1, and then want to include a citation from Firefox 2, it's an awkward process of export and import to move the data across, plus your document will only recognize citations from the FF that was used to write it. So if there is overlap in the content of your databases, and after getting some distance into a project you decide to switch to the other database, you would have to reselect each citation individually.
If that sounds a bit complicated ... it is. :/ Separating work using collections is the way to go.
how do you keep the databases for both projects from loading to the other?