I discovered that I can move .md files in subfolders in /pages or other subfolders of the graph. Logseq use them like they are in the same folder.
So the folder structure in the file system adds another hierarchy that is independent from the others and Logseq is not aware of it.
For me this is another degree of freedom, I like it.
But I would like if Logseq let me choose in which folder a new page is created when I click “New Page”.
And I would also like a full-featured file manager instead of “All Pages” section, where I could move, rename etc the files.