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I want to add comments like

% the following three articles are very interesting
@article{.......

in a .bib file. But every time BibDesk save the file it deletes all comments.

I tried to follow https://tex.stackexchange.com/a/93973/51022 and add some @comment{} entries. But BibDesk move all of them to the beginning of the file, which makes entry-wise comments pointless.

What is the correct way to add comments that survive BibDesk's save? (If it matters, It is BibDesk 1.6.15 on MacOS 10.13.5.)

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    I have used something like: \@article{ref1, title={My Title}, author={Me},year={1993},comment={My comment here}}... I don't really remember if needed something more... Just try it if it fits your needs because I think it will compile in any system/frontend – koleygr Jul 5 '18 at 9:41
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Short answer: you can't do this in BibDesk. The @comment is the only supported form of comment (and % is just ignored by BibTeX; it's not a comment in the grammar). As you found, comments are saved in the preamble of the file.

My recommendation is that you add appropriate metadata to the items themselves, so they can be grouped in categories or found via a search; static groups would be another way to do this. However, groups are not going to be really useful when you look at the file in a text editor.

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