Why not push it under a hidden directory? Like ~/.local/etc? If we're reconstructing some of the hierarchy I think it makes sense to group and hide. Isn't the problem that the home folder is getting cluttered?

Why would I hide them? They're not really special and since I'm organising them with modetc they're not cluttered. For reference, my home looks something like this

    ~
    ├── bin         binaries and scripts
    ├── etc         configuration files
    ├── var
    │   ├── lib     program data
    │   └── cache   program caches
    ├── src         git repositories
    ├── img         pictures
    ├── mail        email in maildir format
    ├── note        text notes, todo
    ├── doc         documents
    └── down        downloads