The solution is simple, stop messing your home and put personal data in
/home/you/personal/
source code in
/home/you/src/
The home is not a place supposed to store random "regular files"
/home/you/personal/
source code in
/home/you/src/
The home is not a place supposed to store random "regular files"
A lot of data is managed by software and by convection there is a dot before them
Unmanaged/Arbitrary data like random pictures or notes are personal and should end up in $HOME/personal
git repos are special managed data, thus they all end up in $HOME/sources
$HOME is supposed to let software to create their data folder and optimally without the dot
The data here includes config (which is read & write like data file)
$HOME/.config or XDG spec is monkey patch that do the wrong thing.
GUI file manager should open $HOME/personal as initial location
Terminal should open $HOME to let user access software's data file with shorter path (aka without .config/ )
You don't know if i am mad or being brilliant or simply brain dead, but i am making perfect scene.
So the next best is to find another place as your home as the OP explains. That's what I do.