When using an existing tex file, without creating a project for it, auxiliary files are not properly dealt with. Specifically, the .aux and/or .bbl files are not found when running bibtex and subsequently latex again.
As a work around, move the .aux file from ~/Library/Application Support/iTeXMac2/Projects.put_aside/.../path.texd to the originating path and symlink back. Then run bibtex from iTeXMac2. Then symlink the .bbl file from the originating path back to ~/Library/Application Support/iTeXMac2/Projects.put_aside/.../path.texd.
Jonathan
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This is precisely something I am currently working on.
iTM2 is indeed limited for those standalone documents,
and you are exactly describing the idea of the workaround I am implemented.
By the way, this problem also shows up for read only documents.
Normally, you would have solved your problem with menu item "File->Project->standard" or something like that.
The effect is to move the stuff stored in the .../Library subfolder to the real location.
I am not sure it works really as expected in absolutely all situations.