wip: claude code and avante

This may be a mistake. We'll see.

Makefile

@@ -1,5 +1,5 @@
 %-darwin:
-	darwin-rebuild --flake ./nix/base-system $*
+	sudo darwin-rebuild --flake ./nix/base-system $*
 
 update-input-%:
-	nix flake lock --update-input $* ./nix/base-system/
+	nix flake update $* ./nix/base-system/

nix/base-system/darwin-configuration.nix

@@ -6,10 +6,11 @@ in
 
   nix = {
     package = pkgs.nix;
+    enable = true;
     # SEE: https://github.com/NixOS/nix/issues/4119#issuecomment-1734738812
     settings.sandbox = "relaxed";
     extraOptions = ''
-      experimental-features = nix-command flakes repl-flake
+      experimental-features = nix-command flakes
       extra-platforms = x86_64-darwin aarch64-darwin x86_64-linux
       trusted-users = root zaphar
     '';
@@ -347,9 +348,6 @@ in
     vfkit
   ];
 
-  # Auto upgrade nix package and the daemon service.
-  services.nix-daemon.enable = true;
-
   #services.spacebar.enable = true;
   #services.spacebar.package = "${pkgs.spacebar}";
 
@@ -365,6 +363,7 @@ in
         (allow file-read* file-write* process-exec mach-lookup (subpath "${builtins.storeDir}"))
       '';
     };
+    system.primaryUser = "zaphar";
   # Used for backwards compatibility, please read the changelog before changing.
   # $ darwin-rebuild changelog
   system.stateVersion = 4;

nix/base-system/flake.lock

@@ -20,6 +20,38 @@
         "type": "github"
       }
     },
+    "avante-src": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1746602870,
+        "narHash": "sha256-REBOplEe2muqfVLwcpTAmXpTrHlzSfhbh8T0litDTDA=",
+        "owner": "yetone",
+        "repo": "avante.nvim",
+        "rev": "113913355a6b9c0fbd62cf52d0cf3e5671d0e34a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "yetone",
+        "repo": "avante.nvim",
+        "type": "github"
+      }
+    },
+    "claude-code-nvim-src": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1749595024,
+        "narHash": "sha256-jKWm3lN5nyZ1BsIKMFt4EQhb0n+iyEyOw79Rj/A3yZI=",
+        "owner": "greggh",
+        "repo": "claude-code.nvim",
+        "rev": "275c47615f4424a0329290ce1d0c18a8320fd8b0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "greggh",
+        "repo": "claude-code.nvim",
+        "type": "github"
+      }
+    },
     "clio-flake": {
       "inputs": {
         "flake-compat": "flake-compat",
@@ -46,6 +78,8 @@
     },
     "custom-flakes": {
       "inputs": {
+        "avante-src": "avante-src",
+        "claude-code-nvim-src": "claude-code-nvim-src",
         "d2-vim-src": "d2-vim-src",
         "flake-utils": "flake-utils_3",
         "gomod2nix-src": "gomod2nix-src",
@@ -62,16 +96,14 @@
         "rust-overlay": "rust-overlay_3",
         "tree-sitter-cli-src": "tree-sitter-cli-src",
         "treesitter-context": "treesitter-context",
-        "victoria-logs-src": "victoria-logs-src",
-        "victoria-metrics-src": "victoria-metrics-src",
         "zig-src": "zig-src"
       },
       "locked": {
-        "lastModified": 1746458473,
-        "narHash": "sha256-3FFhJ18MJFlHHI1YaMKRwXURcQjmLenxIcLFtr+CjGI=",
+        "lastModified": 1751479151,
+        "narHash": "sha256-JxS2yHOiScQQOk8YvK4UAGx68iQJXKnL5qNvV0+9s9A=",
         "owner": "zaphar",
         "repo": "nix-flakes",
-        "rev": "91588e10769e706024d8d03ebb4958c89e00c264",
+        "rev": "0442ff179bd8e82ca3fe713d22e258c89f9caccc",
         "type": "github"
       },
       "original": {
@@ -141,15 +173,16 @@
         ]
       },
       "locked": {
-        "lastModified": 1715871485,
-        "narHash": "sha256-ywapEXmBBI+DVRx/YYC6+6Lk+W8vhShz1uJNvqPKzng=",
+        "lastModified": 1749744770,
+        "narHash": "sha256-MEM9XXHgBF/Cyv1RES1t6gqAX7/tvayBC1r/KPyK1ls=",
         "owner": "lnl7",
         "repo": "nix-darwin",
-        "rev": "cb02884fa1ff5a619a44ab5f1bcc4dedd2d623c2",
+        "rev": "536f951efb1ccda9b968e3c9dee39fbeb6d3fdeb",
         "type": "github"
       },
       "original": {
         "owner": "lnl7",
+        "ref": "nix-darwin-25.05",
         "repo": "nix-darwin",
         "type": "github"
       }
@@ -297,24 +330,6 @@
       "inputs": {
         "systems": "systems_9"
       },
-      "locked": {
-        "lastModified": 1710146030,
-        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "type": "github"
-      }
-    },
-    "flake-utils_11": {
-      "inputs": {
-        "systems": "systems_10"
-      },
       "locked": {
         "lastModified": 1687709756,
         "narHash": "sha256-Y5wKlQSkgEK2weWdOu4J3riRd+kV/VCgHsqLNTTWQ/0=",
@@ -329,7 +344,7 @@
         "type": "github"
       }
     },
-    "flake-utils_12": {
+    "flake-utils_11": {
       "locked": {
         "lastModified": 1649676176,
         "narHash": "sha256-OWKJratjt2RW151VUlJPRALb7OU2S5s+f0vLj4o1bHM=",
@@ -344,9 +359,9 @@
         "type": "github"
       }
     },
-    "flake-utils_13": {
+    "flake-utils_12": {
       "inputs": {
-        "systems": "systems_11"
+        "systems": "systems_10"
       },
       "locked": {
         "lastModified": 1705309234,
@@ -362,9 +377,9 @@
         "type": "github"
       }
     },
-    "flake-utils_14": {
+    "flake-utils_13": {
       "inputs": {
-        "systems": "systems_12"
+        "systems": "systems_11"
       },
       "locked": {
         "lastModified": 1726560853,
@@ -380,9 +395,9 @@
         "type": "github"
       }
     },
-    "flake-utils_15": {
+    "flake-utils_14": {
       "inputs": {
-        "systems": "systems_13"
+        "systems": "systems_12"
       },
       "locked": {
         "lastModified": 1681202837,
@@ -579,23 +594,6 @@
         "type": "github"
       }
     },
-    "harpoon-src": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1706306053,
-        "narHash": "sha256-RjwNUuKQpLkRBX3F9o25Vqvpu3Ah1TCFQ5Dk4jXhsbI=",
-        "owner": "ThePrimeagen",
-        "repo": "harpoon",
-        "rev": "a38be6e0dd4c6db66997deab71fc4453ace97f9c",
-        "type": "github"
-      },
-      "original": {
-        "owner": "ThePrimeagen",
-        "ref": "harpoon2",
-        "repo": "harpoon",
-        "type": "github"
-      }
-    },
     "heracles-flake": {
       "inputs": {
         "flake-compat": "flake-compat_3",
@@ -678,11 +676,11 @@
         "rust-overlay": "rust-overlay_5"
       },
       "locked": {
-        "lastModified": 1737911819,
-        "narHash": "sha256-EsxRZIwe1EaacXj3yp1xo2pqHufr/ZLaqOPnsOmEmI0=",
+        "lastModified": 1749118509,
+        "narHash": "sha256-HKqpDREmzpCskJdfUwvUMJwHTx1RHL7/XMJMUDDMVJA=",
         "owner": "martinvonz",
         "repo": "jj",
-        "rev": "00069119d8165c9c9b3b176c00c3171c73c05138",
+        "rev": "0dc9eb5187b79e3722d20f3c5e2c584edb501e1a",
         "type": "github"
       },
       "original": {
@@ -801,7 +799,7 @@
     },
     "naersk_5": {
       "inputs": {
-        "nixpkgs": "nixpkgs_16"
+        "nixpkgs": "nixpkgs_15"
       },
       "locked": {
         "lastModified": 1650101877,
@@ -819,7 +817,7 @@
     },
     "naersk_6": {
       "inputs": {
-        "nixpkgs": "nixpkgs_17"
+        "nixpkgs": "nixpkgs_16"
       },
       "locked": {
         "lastModified": 1721727458,
@@ -867,28 +865,6 @@
         "type": "github"
       }
     },
-    "neovim-flake": {
-      "inputs": {
-        "flake-utils": "flake-utils_10",
-        "nixpkgs": "nixpkgs_12"
-      },
-      "locked": {
-        "dir": "contrib",
-        "lastModified": 1715862872,
-        "narHash": "sha256-FCOipXHkAbkuFw9JjEpOIJ8BkyMkjkI0Dp+SzZ4yZlw=",
-        "owner": "neovim",
-        "repo": "neovim",
-        "rev": "27fb62988e922c2739035f477f93cc052a4fee1e",
-        "type": "github"
-      },
-      "original": {
-        "dir": "contrib",
-        "owner": "neovim",
-        "ref": "stable",
-        "repo": "neovim",
-        "type": "github"
-      }
-    },
     "nil-flake": {
       "inputs": {
         "flake-utils": "flake-utils_5",
@@ -911,8 +887,8 @@
     },
     "nil-flake_2": {
       "inputs": {
-        "flake-utils": "flake-utils_11",
-        "nixpkgs": "nixpkgs_13",
+        "flake-utils": "flake-utils_10",
+        "nixpkgs": "nixpkgs_12",
         "rust-overlay": "rust-overlay_6"
       },
       "locked": {
@@ -947,27 +923,27 @@
     },
     "nixpkgs-darwin": {
       "locked": {
-        "lastModified": 1735564410,
-        "narHash": "sha256-HB/FA0+1gpSs8+/boEavrGJH+Eq08/R2wWNph1sM1Dg=",
+        "lastModified": 1749596380,
+        "narHash": "sha256-7DEKr2x/jIAKkwHPNNjG6lGUz9nk8SGrbyaeAFMtN34=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "1e7a8f391f1a490460760065fa0630b5520f9cf8",
+        "rev": "210a4a2e3d3853be3a6017e68d2897771fdace35",
         "type": "github"
       },
       "original": {
         "owner": "nixos",
-        "ref": "nixpkgs-24.05-darwin",
+        "ref": "nixpkgs-25.05-darwin",
         "repo": "nixpkgs",
         "type": "github"
       }
     },
     "nixpkgs_10": {
       "locked": {
-        "lastModified": 1737557748,
-        "narHash": "sha256-BaMuhctP1x00+8cBE2cJveJQb70/tWHI50MHj/ZrtOY=",
+        "lastModified": 1747920628,
+        "narHash": "sha256-IlAuXnIi+ZmyS89tt1YOFDCv7FKs9bNBHd3MXMp8PxE=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "606996d74f6e2a12635d41c1bf58bfc7ea3bb5ec",
+        "rev": "e314d5c6d3b3a0f40ec5bcbc007b0cbe412f48ae",
         "type": "github"
       },
       "original": {
@@ -994,22 +970,6 @@
       }
     },
     "nixpkgs_12": {
-      "locked": {
-        "lastModified": 1715787315,
-        "narHash": "sha256-cYApT0NXJfqBkKcci7D9Kr4CBYZKOQKDYA23q8XNuWg=",
-        "owner": "nixos",
-        "repo": "nixpkgs",
-        "rev": "33d1e753c82ffc557b4a585c77de43d4c922ebb5",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nixos",
-        "ref": "nixos-unstable",
-        "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
-    "nixpkgs_13": {
       "locked": {
         "lastModified": 1690441914,
         "narHash": "sha256-Ac+kJQ5z9MDAMyzSc0i0zJDx2i3qi9NjlW5Lz285G/I=",
@@ -1025,23 +985,23 @@
         "type": "github"
       }
     },
-    "nixpkgs_14": {
+    "nixpkgs_13": {
       "locked": {
-        "lastModified": 1738579205,
-        "narHash": "sha256-o6BeeanSUALvz8oL2CHOikVjCf7j+HqlA0WGvKOUX3Q=",
+        "lastModified": 1749747690,
+        "narHash": "sha256-FPhMfYq+ngKpZiYaOblqR6S9z9JVpTlW8EaQ98xwkkU=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "be5cf18b3d26ba2db938a72ade93ac8a9a7462ff",
+        "rev": "f7d4856c2d1af130193777964535304fdc76e368",
         "type": "github"
       },
       "original": {
         "owner": "nixos",
-        "ref": "release-24.11",
+        "ref": "release-25.05",
         "repo": "nixpkgs",
         "type": "github"
       }
     },
-    "nixpkgs_15": {
+    "nixpkgs_14": {
       "locked": {
         "lastModified": 1689850295,
         "narHash": "sha256-fUYf6WdQlhd2H+3aR8jST5dhFH1d0eE22aes8fNIfyk=",
@@ -1057,7 +1017,7 @@
         "type": "github"
       }
     },
-    "nixpkgs_16": {
+    "nixpkgs_15": {
       "locked": {
         "lastModified": 1650109093,
         "narHash": "sha256-tqlnKrAdJktRLXTou9le0oTqrYBAFpGscV5RADdpArU=",
@@ -1071,6 +1031,20 @@
         "type": "indirect"
       }
     },
+    "nixpkgs_16": {
+      "locked": {
+        "lastModified": 1729658218,
+        "narHash": "sha256-9Rg+AqLqvqqJniP/OQB3GtgXoAd8IlazsHp97va042Y=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "dfffb2e7a52d29a0ef8e21ec8a0f30487b227f1a",
+        "type": "github"
+      },
+      "original": {
+        "id": "nixpkgs",
+        "type": "indirect"
+      }
+    },
     "nixpkgs_17": {
       "locked": {
         "lastModified": 1729658218,
@@ -1086,20 +1060,6 @@
       }
     },
     "nixpkgs_18": {
-      "locked": {
-        "lastModified": 1729658218,
-        "narHash": "sha256-9Rg+AqLqvqqJniP/OQB3GtgXoAd8IlazsHp97va042Y=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "dfffb2e7a52d29a0ef8e21ec8a0f30487b227f1a",
-        "type": "github"
-      },
-      "original": {
-        "id": "nixpkgs",
-        "type": "indirect"
-      }
-    },
-    "nixpkgs_19": {
       "locked": {
         "lastModified": 1682109806,
         "narHash": "sha256-d9g7RKNShMLboTWwukM+RObDWWpHKaqTYXB48clBWXI=",
@@ -1253,7 +1213,7 @@
     },
     "nurl-flake_2": {
       "inputs": {
-        "nixpkgs": "nixpkgs_15"
+        "nixpkgs": "nixpkgs_14"
       },
       "locked": {
         "lastModified": 1701273941,
@@ -1277,14 +1237,12 @@
         "d2-vim-src": "d2-vim-src_2",
         "darwin": "darwin_2",
         "durnitisp-flake": "durnitisp-flake",
-        "harpoon-src": "harpoon-src",
         "heracles-flake": "heracles-flake",
         "jujutsu-flake": "jujutsu-flake",
         "mcphub-flake": "mcphub-flake",
         "neogit-src": "neogit-src_2",
-        "neovim-flake": "neovim-flake",
         "nil-flake": "nil-flake_2",
-        "nixpkgs": "nixpkgs_14",
+        "nixpkgs": "nixpkgs_13",
         "nixpkgs-darwin": "nixpkgs-darwin",
         "nurl-flake": "nurl-flake_2",
         "roslyn-lsp": "roslyn-lsp_2",
@@ -1292,7 +1250,6 @@
         "rust-overlay-flake": "rust-overlay-flake",
         "sheetsui-flake": "sheetsui-flake",
         "sile-flake": "sile-flake",
-        "treesitter-context": "treesitter-context_2",
         "unstable": "unstable"
       }
     },
@@ -1333,7 +1290,7 @@
     "runwhen-flake": {
       "inputs": {
         "flake-compat": "flake-compat_4",
-        "flake-utils": "flake-utils_12",
+        "flake-utils": "flake-utils_11",
         "naersk": "naersk_5"
       },
       "locked": {
@@ -1375,7 +1332,7 @@
     },
     "rust-overlay-flake": {
       "inputs": {
-        "flake-utils": "flake-utils_13",
+        "flake-utils": "flake-utils_12",
         "nixpkgs": [
           "nixpkgs"
         ]
@@ -1469,11 +1426,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1737685583,
-        "narHash": "sha256-p+NVABRpGi+pT+xxf9HcLcFVxG6L+vEEy+NwzB9T0f8=",
+        "lastModified": 1747967795,
+        "narHash": "sha256-76s4jDRbQzxRO+5y8ilMp5V30qVgY9R6n8U7aOap8ig=",
         "owner": "oxalica",
         "repo": "rust-overlay",
-        "rev": "eb64cbcc8eee0fa87ebded92805280d2ec97415a",
+        "rev": "f1d5bfa8c692cacd798a3e1fb93d54c1b9ac701a",
         "type": "github"
       },
       "original": {
@@ -1530,9 +1487,9 @@
     },
     "sheetsui-flake": {
       "inputs": {
-        "flake-utils": "flake-utils_14",
+        "flake-utils": "flake-utils_13",
         "naersk": "naersk_6",
-        "nixpkgs": "nixpkgs_18",
+        "nixpkgs": "nixpkgs_17",
         "rust-overlay": "rust-overlay_7"
       },
       "locked": {
@@ -1552,10 +1509,10 @@
     "sile-flake": {
       "inputs": {
         "flake-compat": "flake-compat_5",
-        "flake-utils": "flake-utils_15",
+        "flake-utils": "flake-utils_14",
         "gitignore": "gitignore",
         "libtexpdf-src": "libtexpdf-src",
-        "nixpkgs": "nixpkgs_19"
+        "nixpkgs": "nixpkgs_18"
       },
       "locked": {
         "lastModified": 1694595810,
@@ -1631,21 +1588,6 @@
         "type": "github"
       }
     },
-    "systems_13": {
-      "locked": {
-        "lastModified": 1681028828,
-        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
-        "owner": "nix-systems",
-        "repo": "default",
-        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-systems",
-        "repo": "default",
-        "type": "github"
-      }
-    },
     "systems_2": {
       "locked": {
         "lastModified": 1681028828,
@@ -1799,30 +1741,13 @@
         "type": "github"
       }
     },
-    "treesitter-context_2": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1693236978,
-        "narHash": "sha256-B6BXeFEWxTFf46JrlatsxEQcC6+/hPIDBb5cIcJpLZg=",
-        "owner": "nvim-treesitter",
-        "repo": "nvim-treesitter-context",
-        "rev": "e6b743ccd4e780bc9cd85b707de67df72eea1a23",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nvim-treesitter",
-        "repo": "nvim-treesitter-context",
-        "rev": "e6b743ccd4e780bc9cd85b707de67df72eea1a23",
-        "type": "github"
-      }
-    },
     "unstable": {
       "locked": {
-        "lastModified": 1746152631,
-        "narHash": "sha256-zBuvmL6+CUsk2J8GINpyy8Hs1Zp4PP6iBWSmZ4SCQ/s=",
+        "lastModified": 1751349533,
+        "narHash": "sha256-5XRh0mB06/7WYDLu9ZXsx1GhyvvNVZDtPyg34sUCLJs=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "032bc6539bd5f14e9d0c51bd79cfe9a055b094c3",
+        "rev": "bdfd0f2afcf764e531d0960c821ab070a6174b15",
         "type": "github"
       },
       "original": {
@@ -1830,40 +1755,6 @@
         "type": "indirect"
       }
     },
-    "victoria-logs-src": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1742084154,
-        "narHash": "sha256-Oxy4MntciWUij83zyHixlEDa1DgeG/2ntNN+Nbw8xJg=",
-        "owner": "VictoriaMetrics",
-        "repo": "VictoriaMetrics",
-        "rev": "771233ebcd706578c44ed82047c714381a75ab5a",
-        "type": "github"
-      },
-      "original": {
-        "owner": "VictoriaMetrics",
-        "ref": "v1.17.0-victorialogs",
-        "repo": "VictoriaMetrics",
-        "type": "github"
-      }
-    },
-    "victoria-metrics-src": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1742560966,
-        "narHash": "sha256-iOeGz0qDeKMdafTDqI4/IMkXZ6KLdMDtFie3jwv2uvU=",
-        "owner": "VictoriaMetrics",
-        "repo": "VictoriaMetrics",
-        "rev": "e950846534ea594940a0f69845ef60a053c98ffd",
-        "type": "github"
-      },
-      "original": {
-        "owner": "VictoriaMetrics",
-        "ref": "v1.114.0",
-        "repo": "VictoriaMetrics",
-        "type": "github"
-      }
-    },
     "zig-src": {
       "flake": false,
       "locked": {

nix/base-system/flake.nix

@@ -1,15 +1,15 @@
 {
   inputs = {
     # Default to sane nixpkgs versions
-    nixpkgs.url = "github:nixos/nixpkgs/release-24.11";
+    nixpkgs.url = "github:nixos/nixpkgs/release-25.05";
     unstable.url = "nixpkgs";
-    nixpkgs-darwin.url = "github:nixos/nixpkgs/nixpkgs-24.05-darwin";
+    nixpkgs-darwin.url = "github:nixos/nixpkgs/nixpkgs-25.05-darwin";
     #lean4-flake = { 
     #  url = "github:leanprover/lean4/v4.4.0";
     #  inputs.nixpkgs.follows = "nixpkgs";
     #};
     darwin = {
-      url = "github:lnl7/nix-darwin";
+      url = "github:lnl7/nix-darwin/nix-darwin-25.05";
       # ensure that darwinSystem uses our nixpkgs version
       inputs.nixpkgs.follows = "nixpkgs-darwin";
     };
@@ -31,20 +31,16 @@
       inputs.nixpkgs.follows = "nixpkgs";
     };
 
-    neovim-flake = {
-        url = "github:neovim/neovim/stable?dir=contrib";
-        # NOTE(jeremy): Currently this needs a newer nixpkgs version
-        #inputs.nixpkgs.follows = "nixpkgs";
-    };
+    #neovim-flake = {
+    #    url = "github:neovim/neovim/stable?dir=contrib";
+    #    # NOTE(jeremy): Currently this needs a newer nixpkgs version
+    #    #inputs.nixpkgs.follows = "nixpkgs";
+    #};
     jujutsu-flake.url = "github:martinvonz/jj";
     custom-flakes = {
         url = "github:zaphar/nix-flakes";
         inputs.nixpkgs.follows = "nixpkgs";
     };
-    harpoon-src = {
-        url = "github:ThePrimeagen/harpoon/harpoon2";
-        flake = false;
-    };
     neogit-src = {
         url = "github:NeogitOrg/neogit";
         flake = false;
@@ -53,11 +49,6 @@
         url = "github:terrastruct/d2-vim";
         flake = false;
     };
-    # We need to pin to this version of treesitter because it breaks after this revision
-    treesitter-context = {
-        url = "github:nvim-treesitter/nvim-treesitter-context/e6b743ccd4e780bc9cd85b707de67df72eea1a23";
-        flake = false;
-    };
     roslyn-lsp = {
         url = "github:zaphar/roslyn.nvim/main";
         flake = false;
@@ -76,11 +67,9 @@
     agenix-flake,
     nil-flake,
     nurl-flake,
-    harpoon-src,
     custom-flakes,
     unstable,
     heracles-flake,
-    neovim-flake,
     clio-flake,
     sheetsui-flake,
     mcphub-flake,
@@ -90,27 +79,18 @@
     vimModule = system: let
       nil-pkg = nil-flake.packages."${system}".default;
       mcp-hub-binary = custom-flakes.packages."${system}".mcp-hub;
+      claude-code-binary = custom-flakes.packages."${system}".claude-code;
     in
     { config, pkgs, ...}: let
         unstablePkgs = import unstable { inherit system; };
-        possession-nvim = pkgs.callPackage ./possession-nvim.nix {
-            inherit (pkgs.vimUtils) buildVimPlugin;
-			      inherit (pkgs) fetchFromGitHub;
-        };
-        harpoon-nvim = pkgs.vimUtils.buildVimPlugin {
-          pname = "harpoon";
-          version = "2024-01-28";
-          src = harpoon-src;
-        };
         neogit-nvim = custom-flakes.packages."${system}".neogit-nvim;
         d2-vim = custom-flakes.packages."${system}".d2-vim;
         hunk-nvim = custom-flakes.packages."${system}".hunk-nvim;
         # TODO(zaphar): Apparently this is a remote plugin so it needs some additional love.
         #nvim-bnf = custom-flakes.packages."${system}".nvim-bnf;
-        nvim-treesitter-context = custom-flakes.packages."${system}".nvim-treesitter-context;
         roslyn-nvim = custom-flakes.packages."${system}".roslyn-nvim;
         ionide-nvim = custom-flakes.packages."${system}".ionide-nvim;
-        nvim = neovim-flake.packages."${system}".neovim;
+        claude-code-nvim = custom-flakes.packages."${system}".claude-code-nvim;
         # TODO(zaphar): Until nixpkgs update to a newer version of tree-sitter the queries will be wrong
         # for csharp
         #tree-sitter-csharp = pkgs.callPackage ./nvim-treesitter-csharp.nix {
@@ -137,17 +117,14 @@
      
         nixpkgs.overlays = [
             (final: prev: {
-                custom-neovim = nvim;
                 lorri = unstablePkgs.lorri;
-                avante-nvim = unstablePkgs.vimPlugins.avante-nvim;
-                copilot-lua = unstablePkgs.vimPlugins.copilot-lua;
             })
         ];
-        programs = with pkgs; {
+        programs = with unstablePkgs; {
           neovim.enable = true;
           neovim.vimAlias = true;
           neovim.viAlias = true;
-          neovim.package = pkgs.custom-neovim;
+          neovim.package = unstablePkgs.neovim-unwrapped;
           neovim.configure = {
           customRC = "lua << EOF
 ${builtins.readFile ./init.lua}
@@ -224,9 +201,8 @@ EOF";
               vim-dasht
               direnv-vim
               mcphub-nvim
+              claude-code-nvim
             ]) ++ [
-              possession-nvim
-              harpoon-nvim
               d2-vim
               hunk-nvim
               neogit-nvim
@@ -237,9 +213,9 @@ EOF";
         };
         environment.systemPackages = (with pkgs; [
             terraform-ls
+            tinymist
             nodePackages.typescript-language-server
             nodePackages.jsdoc
-            python312Packages.jedi-language-server
             # TODO find a version of the julia package that will install
             # on darwin and add it as an overlay
             nil-pkg
@@ -251,6 +227,7 @@ EOF";
             devenv
             unstablePkgs.fq
             mcp-hub-binary
+            claude-code-binary
         ]);
       };
     };
@@ -292,6 +269,7 @@ EOF";
             uv = unstablePkgs.uv;
             quint = (pkgs.callPackage ../packages/quint/default.nix {})."@informalsystems/quint";
             quint-lsp = (pkgs.callPackage ../packages/quint/default.nix {})."@informalsystems/quint-language-server";
+            ollama = unstablePkgs.ollama;
           })
           rust-overlay
         ];
@@ -318,13 +296,11 @@ EOF";
           };
         };
         environment.systemPackages = (with pkgs; [
-            isabelle
             sheetsui
             lean4
             quint
             quint-lsp
             terraform # TODO(jeremy): Replace with opentofu when that is an option.
-            nomad
             oha
             nodejs
             gnumake

nix/base-system/init.lua

@@ -20,6 +20,10 @@ vim.opt.fileformats = "unix,dos"
 -- Recommended by Avante docs
 -- views can only be fully collapsed with the global statusline
 vim.opt.laststatus = 3
+-- formatexpr defaulted to the lsp provider by default recently
+-- which breaks `gq` and company paragraph formatting in non lsp
+-- contexts.
+vim.opt.formatexpr = ""
 
 vim.g.BASH_AuthorName = 'Jeremy Wall'
 vim.g.BASH_AuthorRef = 'jw'
@@ -43,6 +47,23 @@ vim.api.nvim_create_autocmd({ "BufEnter", "BufWinEnter" }, {
     end,
 })
 
+vim.api.nvim_create_autocmd({ "BufNewfile", "BufRead" }, {
+    callback = function(args)
+        -- If treesitter supports this filetype then use the treesitter fold expression
+        local ft = vim.bo.filetype
+        if ft and ft ~= "" then
+            -- Safely check if a parser exists for this filetype
+            local has_parser = pcall(function() return vim.treesitter.language.inspect(ft) end)
+            if has_parser then
+                vim.wo.foldexpr = 'v:lua.vim.treesitter.foldexpr()'
+                vim.wo.foldmethod = 'expr'
+                vim.wo.foldlevel = 10
+            end
+        end
+    end,
+})
+
+
 vim.cmd([[
 au BufNewFile,BufRead *Makefile,*.mk set noexpandtab
 ]])
@@ -147,23 +168,26 @@ local caps = vim.tbl_deep_extend(
 
 local lspconfig = require("lspconfig")
 
+local configure_lsp = function(name, config)
+    vim.lsp.enable(name)
+    vim.lsp.config(name, config)
+end
+
 -- Typst
-lspconfig.tinymist.setup {
+configure_lsp('tinymist', {
     capabilities = caps,
     settings = {
         exportPdf = "onSave",
     },
-}
+})
 
 -- Terraform lsp setup
-lspconfig.terraformls.setup {}
+configure_lsp('terraformls', {})
 
 -- Nix language server support
-lspconfig.nil_ls.setup {
+configure_lsp('nil_ls', {
     capabilities = caps,
-}
-
-lspconfig.jedi_language_server.setup {}
+})
 
 require('roslyn').setup({
     --                    client, bufnr
@@ -175,23 +199,14 @@ require('roslyn').setup({
     log_level = "Trace",
 });
 
---ocaml
-lspconfig.ocamllsp.setup {
-    capabilities = caps
-}
-
--- Java language server support
-lspconfig.java_language_server.setup {
-    capabilities = caps
-}
-
 -- Typescript language server support
-lspconfig.tsserver.setup {
+configure_lsp('tsserver', {
+    cmd = { 'typescript-language-server', '--stdio' },
     capabilities = caps
-}
+})
 
 -- Rust language server support
-lspconfig.rust_analyzer.setup {
+configure_lsp('rust_analyzer', {
     settings = {
         -- https://github.com/rust-lang/rust-analyzer/blob/master/docs/user/generated_config.adoc
         ['rust-analyzer'] = {
@@ -199,10 +214,11 @@ lspconfig.rust_analyzer.setup {
         }
     },
     capabilities = caps
-}
+})
 
 -- lua language server setup.
-lspconfig.lua_ls.setup {
+configure_lsp('lua_ls', {
+    cmd = { 'lua-language-server' },
     settings = {
         Lua = {
             runtime = { version = 'LuaJIT', },
@@ -222,7 +238,13 @@ lspconfig.lua_ls.setup {
         },
     },
     capabilities = caps
-}
+})
+
+configure_lsp('ty', {
+  cmd = { 'ty', 'server' },
+  filetypes = { 'python' },
+  root_markers = { 'ty.toml', 'pyproject.toml', '.git' },
+})
 
 -- lsp configuration
 vim.api.nvim_create_autocmd('LspAttach', {
@@ -238,6 +260,10 @@ vim.api.nvim_create_autocmd('LspAttach', {
         if client and client.server_capabilities.codelens then
             vim.lsp.codelens.refresh()
         end
+        -- formatexpr defaulted to the lsp provider by default recently
+        -- which breaks `gq` and company paragraph formatting in non lsp
+        -- contexts.
+        vim.bo[args.buf].formatexpr = ""
     end,
 })
 
@@ -255,22 +281,8 @@ vim.api.nvim_create_autocmd({ 'BufEnter', 'InsertLeave', 'CursorHold' }, {
 })
 
 -- LSP Diagnostics Options Setup
-local sign = function(opts)
-    vim.fn.sign_define(opts.name, {
-        texthl = opts.name,
-        text = opts.text,
-        numhl = ''
-    })
-end
-
-sign({ name = 'DiagnosticSignError', text = '🔥' })
-sign({ name = 'DiagnosticSignWarn', text = '⚠️' })
-sign({ name = 'DiagnosticSignHint', text = '➡️' })
-sign({ name = 'DiagnosticSignInfo', text = '🗒️' })
-
 vim.diagnostic.config({
     virtual_text = false,
-    signs = true,
     update_in_insert = true,
     underline = true,
     severity_sort = false,
@@ -280,6 +292,14 @@ vim.diagnostic.config({
         header = '',
         prefix = '',
     },
+    signs = {
+        text =  {
+            [vim.diagnostic.severity.ERROR] = '🔥',
+            [vim.diagnostic.severity.WARN] = '⚠️',
+            [vim.diagnostic.severity.HINT] = '➡️',
+            [vim.diagnostic.severity.INFO] = '🗒️',
+        },
+    }
 })
 
 vim.cmd([[
@@ -320,31 +340,55 @@ require('nvim-treesitter.configs').setup {
         extended_mode = true,
         max_file_lines = nil,
     },
-    --textobjects = {
-    --  enable = true,
-    --  select = {
-    --    enable = true,
-    --    lookahead = true, -- Automatically jump forward to textobj, similar to targets.vim
-    --    keymaps = {
-    --      -- You can use the capture groups defined in textobjects.scm
-    --      ['aa'] = '@parameter.outer',
-    --      ['ia'] = '@parameter.inner',
-    --      ['af'] = '@function.outer',
-    --      ['if'] = '@function.inner',
-    --      ['ac'] = '@class.outer',
-    --      ['ic'] = '@class.inner',
-    --    },
-    --  },
-    --},
-    --incremental_selection = {
-    --  enable = true,
-    --  keymaps = {
-    --    init_selection = '<Leader>c',
-    --    node_incremental = '<Leader>c',
-    --    scope_incremental = '<Leader>ci',
-    --    node_decremental = '<Leader>cx',
-    --  },
-    --},
+    textobjects = {
+      move = {
+        enable = true,
+        set_jumps = true, -- whether to set jumps in the jumplist
+        goto_next_start = {
+          ["]m"] = "@function.outer",
+          ["]]"] = { query = "@class.outer", desc = "Next class start" },
+          --
+          -- You can use regex matching (i.e. lua pattern) and/or pass a list in a "query" key to group multiple queries.
+          ["]o"] = "@loop.*",
+          -- ["]o"] = { query = { "@loop.inner", "@loop.outer" } }
+          --
+          -- You can pass a query group to use query from `queries/<lang>/<query_group>.scm file in your runtime path.
+          -- Below example nvim-treesitter's `locals.scm` and `folds.scm`. They also provide highlights.scm and indent.scm.
+          ["]s"] = { query = "@local.scope", query_group = "locals", desc = "Next scope" },
+          ["]z"] = { query = "@fold", query_group = "folds", desc = "Next fold" },
+        },
+        goto_next_end = {
+          ["]M"] = "@function.outer",
+          ["]["] = "@class.outer",
+        },
+        goto_previous_start = {
+          ["[m"] = "@function.outer",
+          ["[["] = "@class.outer",
+        },
+        goto_previous_end = {
+          ["[M"] = "@function.outer",
+          ["[]"] = "@class.outer",
+        },
+        -- Below will go to either the start or the end, whichever is closer.
+        -- Use if you want more granular movements
+        -- Make it even more gradual by adding multiple queries and regex.
+        goto_next = {
+          ["]d"] = "@conditional.outer",
+        },
+        goto_previous = {
+          ["[d"] = "@conditional.outer",
+        }
+      },
+    },
+    incremental_selection = {
+      enable = true,
+      keymaps = {
+        init_selection = '<Leader>c',
+        node_incremental = '<Leader>c',
+        scope_incremental = '<Leader>ci',
+        node_decremental = '<Leader>cx',
+      },
+    },
 }
 
 require 'treesitter-context'.setup {
@@ -467,33 +511,6 @@ vim.keymap.set("n", "<Leader>ga", function()
     vim.cmd("!git add %")
 end)
 
-require('possession').setup {
-    commands = {
-        save = 'SSave',
-        load = 'SLoad',
-        delete = 'SDelete',
-        list = 'SList',
-    },
-    autosave = {
-        current = true,
-        on_load = true,
-        on_quit = true,
-    },
-    telescope = {
-        list = {
-            default_action = 'load',
-            mappings = {
-                save = { n = '<c-x>', i = '<c-x>' },
-                load = { n = '<c-v>', i = '<c-v>' },
-                delete = { n = '<c-t>', i = '<c-t>' },
-                rename = { n = '<c-r>', i = '<c-r>' },
-            },
-        },
-    },
-}
-
-
-telescope.load_extension('possession')
 -- https://github.com/nvim-telescope/telescope.nvim
 telescope.setup({
     defaults = {
@@ -515,9 +532,6 @@ telescope.setup({
     },
 })
 
-local harpoon = require('harpoon')
-
-harpoon:setup()
 
 local lean = require 'lean'
 
@@ -536,7 +550,6 @@ lean.setup {
 }
 
 -- telescope keymaps
-vim.keymap.set("n", "<Leader>pl", telescope.extensions.possession.list)
 -- TODO(zaphar): Remove this once my muscle memory has set in.
 vim.keymap.set("n", "<Leader>nff", telescope_builtins.fd)
 vim.keymap.set("n", "<Leader>ff", telescope_builtins.fd)
@@ -552,11 +565,6 @@ end)
 vim.keymap.set("n", "<leader>lds", telescope_builtins.lsp_document_symbols, { desc = "[D]ocument [S]ymbols" })
 vim.keymap.set("n", "<leader>lws", telescope_builtins.lsp_dynamic_workspace_symbols, { desc = "[W]orkspace [S]ymbols" })
 
--- harpoon keymaps
-vim.keymap.set("n", "<Leader>ha", function() harpoon:list():append() end)
-vim.keymap.set("n", "<Leader>he", function() harpoon.ui:toggle_quick_menu(harpoon:list()) end)
-vim.keymap.set("n", "<Leader>hj", function() harpoon:list():prev() end)
-vim.keymap.set("n", "<Leader>hk", function() harpoon:list():next() end)
 
 -- codelens keymaps
 vim.keymap.set("n", "<Leader>rr", vim.lsp.codelens.run)
@@ -706,7 +714,7 @@ function get_server_list_prompt(hub_instance)
     for _, server in ipairs(servers) do
         mcp_tool_prompt = mcp_tool_prompt .. "## server name: `" .. server.name .. "`\n\n"
 
-        if server.capabilities.tools and #server.capabilities.tools > 0 then
+        if server.capabilities and server.capabilities.tools and #server.capabilities.tools > 0 then
             mcp_tool_prompt = mcp_tool_prompt .. "Available tools:\n\n"
             for _, tool in ipairs(server.capabilities.tools) do
                 mcp_tool_prompt = mcp_tool_prompt .. "- tool name: `" .. tool.name .. "`\n"
@@ -733,7 +741,32 @@ function update_avante_system_prompt()
     end
 end
 
-require('copilot').setup();
+vim.keymap.set("n", "<Leader>ab", function() require('avante').get().file_selector:add_buffer_files() end)
+vim.keymap.set("n", "<Leader>af", function() require('avante').get().file_selector:add_current_buffer() end)
+
+get_root_dir = function()
+    -- First try to get the root path from LSP
+    local bufnr = vim.api.nvim_get_current_buf()
+    local clients = vim.lsp.get_clients({ bufnr = bufnr })
+    
+    -- Check if we have an active LSP client with a root_dir
+    for _, client in ipairs(clients) do
+        if client.config and client.config.root_dir then
+            return client.config.root_dir
+        end
+    end
+    
+    -- Fall back to file-based detection
+    local root_file = vim.fs.find(function(name, path)
+        return name:match('(pyproject.toml|.sln|Cargo.toml|.git)$')
+    end, { upward = true })[1]
+    
+    return root_file and vim.fs.dirname(root_file) or vim.fn.getcwd()
+end
+
+require('copilot').setup({
+    root_dir = get_root_dir,
+})
 
 require('avante').setup({
     provider = "claude",
@@ -752,6 +785,12 @@ require('avante').setup({
     behavior = {
         enable_cursor_planning_mode = true,
     },
+    windows = {
+        ask = {
+            start_insert=false,
+            focus_on_apply="theirs",
+        },
+    },
     system_prompt = make_avante_system_prompt(mcphub.get_hub_instance()),
     custom_tools = { require("mcphub.extensions.avante").mcp_tool() },
     -- Disable these because we'll use the mcphub versions instead