There are many lists of the usual order of adjectives on the internet, some clearer than others. The Cambridge Dictionary one being one of the clearer ones. All of them, though, have the same order which the Cambridge Dictionary says is
Opinion, size, physical quality, shape age, colour, origin, material, type, purpose
(although some lists insert "determiner" at the front to account for articles and counts like 'a', 'the', 'one', 'many' and so on.)
The problem with your set of three adjectives is that it is difficult to decide which category lean and minimalist belong to. This is partly because, I suspect, you are talking about a software tool and the words 'lean' and 'minimalist' have specific meanings in IT which are slightly different from their general meanings. Also 'small' and 'lean' could both describe physical properties of something, but software doesn't have a physical property apart from its size in bytes.
"Small", presumably, refers to size in bytes. If this is the case it should be a long way up the list, probably appearing first unless there was an adjective in the list expressing an opinion such as 'wonderful', 'essential', 'useful' and so on.
"Lean" would, if you were referring to something physical, be a physical quality. For instance "his lean body", "a piece of lean meat" and so on so it would come in the third category. For the purposes of this exercise you could treat it as though it was being used normally but you could also say that it was a description of the type of software.
"Minimalist" is the most difficult one to classify because it could be said to an opinion (in which case it would come first) or it could be said to be a description of a type in which case it would come at or near the end. For instance we could of "a minimalist red plastic chair" or "a red plastic minimalist chair" depending on how we were using "minimalist". In the case of software I would suggest that it is a description of the type of software.
If you consider that both 'lean' and 'minimalist' describe the type of software (which would be my preference) you then have to decide how to place them within the same category. I would suggest that you place 'lean' first as it is the shorter and, probably to most people, the more familiar word. I would also join them with the conjunction 'and' to emphasise their equal status in the list.
This would give you the description "Nano is a small, lean and minimalist tool."
A word of warning, though. The list of adjective categories is often presented to non native learners of English as though it was a rigid, unbreakable, sequence that has to be learned thoroughly and adhered to strictly but native speakers don't use the list at all, in fact most native speakers don't even know that it exists. The list does reflect the reality of the way we use adjectives but we do it automatically and do, sometimes, diverge from the taught order. If possible listen to and read lots of English to get the feel for how it's done.
