chore: complete AGENTS.md documentation

- Add comprehensive project documentation to AGENTS.md
- Remove stale docs from docs/ directory
- Update agent configs (agents.nix, pi.nix)
- Update python.nix language config
- Update .gitignore

home/coding/languages/python.nix

@@ -19,12 +19,15 @@ in {
   };
 
   config = mkIf cfg.enable {
-    home.packages = [
+    home.packages = with pkgs; [
       (pkgs.python3.withPackages (ps:
-        with ps; [
-          pip
-          uv
-        ] ++ cfg.extraPackages))
+        with ps;
+          [
+            pip
+            uv
+          ]
+          ++ cfg.extraPackages))
+      pyrefly
     ];
   };
 }