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?
~
├── 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 downloadsBut more I was thinking that having ~/bin ~/etc ~/src and so on is just clutter. I use ~/.local/{bin,build,lib} so it's compact and reduces clutter in my home