refactor: reorganize, add package (opencode, osgrep, beads), add ai agent shell

devshells/jupyter-notebook.nix

@@ -1,31 +0,0 @@
-{ pkgs, python ? pkgs.python312, ... }:
-
-let
-  # Python environment with notebook tooling and core data-science libs
-  pythonWithNotebook = python.withPackages (ps:
-    with ps; [
-      altair
-      ipykernel
-      jupyterlab
-      matplotlib
-      numpy
-      pandas
-      polars
-      plotly
-      scipy
-      scikit-learn
-      seaborn
-    ]);
-in pkgs.mkShell {
-  name = "jupyter-notebook";
-  packages = [ pythonWithNotebook pkgs.ruff pkgs.pyright pkgs.git ];
-  shellHook = ''
-    export PYTHONNOUSERSITE=1
-    export JUPYTER_CONFIG_DIR="''${XDG_CONFIG_HOME:-$HOME/.config}/jupyter"
-    mkdir -p "$JUPYTER_CONFIG_DIR"
-    echo "Jupyter notebook shell ready"
-    echo "Python: ${python.version}"
-    echo "Launch notebook: jupyter lab"
-    echo "Launch classic: jupyter notebook"
-  '';
-}