@alex0 I haven’t fully thought this through, but another option could be to keep Logseq links “[[]]” as they are, referring to local storage with unique names, but make Logseq recursively follow file:// links to .md (or .lq) files and incorporate them into the graph.
The advantage would be that any files in any folders could be part of the graph, even for regular Markdown files that don’t follow Logseq’s extensions.
This way there would be two namespaces, one for [[]] and one using regular relative links.
I am not sure this is worth it.
There is another feature request in the pipeline on Cross graph referencing. Not clear how this will be implemented, but it might at least allow to have separate graphs for individual projects, as suggested by @memeplex.