We tried to make OpenKM as intuitive as possible, but an advice is always welcome.
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In community version this feature has not been included. You should modify source code to do it. For what do you want it, because other option is doing directly to database, but I suppose will not solve your problem.
I need to keep in OpenKM some doc, xls, pdf, jpg and so on files with meta information.
That info will be, what have in file. And after I will need to find right file quickly.
Directory organization will not give to me that flexibility.
Can you share here the metadata definition and some screenshot with values. I would like to test in some of our dev environements. We do not need everything, minimal metadata definition and values into are enought.