Are markdown files becoming the new dot files?

When you look at projects like Symfony , Astro or Ollama the first thing you see, after directories, are dot files. Some tools abandoned the dot prefix and just use yaml or json files, and a rare xml file. With AI tools we are seeing CLAUDE.md, AGENTS.md and other markdown files appear in the root directory. For me this is straw that broke the camel's back. The problem I have with the markdown files are the same that I have with the non-dot files, they miss context. Dot files and folders are an old convention to signal configuration. Most tools that use those configuration files have an option to specify the file. So it is possible to create a .tools folders and move all those files to that folder. Then use a makeFile to alias the tools with the config file. The same could be done for AI markdown files. The strange thing I discovered with Claude code is that it can use a .claude folder where you can place the config. But for scoping you need to add CLAUDE.md files to subfolders, this i