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Have you tried zk (https://github.com/mickael-menu/zk)? I have there markdown files with random filenames in single directory (not mandatory) - so no organization on the filesystem level. But I use tags and links and zk provides me tools for organization according to them. Also editor integration for it exists (https://github.com/mickael-menu/zk/blob/main/docs/editors-integration.md).
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