fix nix functional test & add mole to brew, del osgrep bd

flake.nix

@@ -140,7 +140,7 @@
           else
             pkgs.python3;
 
-          # Custom packages (osgrep, beads, etc.)
+          # Custom packages
           customPkgs = import ./packages { inherit pkgs lib llm-agents; };
 
           # Common arguments passed to all devshell imports
@@ -173,6 +173,6 @@
         let
           pkgs = mkPkgs system;
           customPkgs = import ./packages { inherit pkgs lib llm-agents; };
-        in { inherit (customPkgs) osgrep opencode beads; });
+        in { inherit (customPkgs) opencode; });
     };
 }

modules/darwin/homebrew.nix

@@ -16,7 +16,7 @@ in {
     };
     brews = mkOption {
       type = types.listOf types.str;
-      default = [ "curl" "yt-dlp" "infisical" ];
+      default = [ "curl" "yt-dlp" "infisical" "mole" ];
       description = "Homebrew formulae to install.";
     };
     casks = mkOption {

modules/darwin/system.nix

@@ -2,7 +2,7 @@
   imports = [ ./homebrew.nix ./devtools.nix ];
 
   nix = {
-    package = pkgs.nix;
+    package = pkgs.nixVersions.nix_2_28;
     extraOptions = ''
       keep-derivations = true
       keep-outputs = true

modules/home/programs/neovim.nix

@@ -21,6 +21,7 @@
       nil # Nix LSP
       pyright
       nodePackages.typescript-language-server
+      mdx-language-server
       rust-analyzer
       gopls
       clang-tools # provides clangd

modules/home/programs/nvim/lua/plugins/formatting.lua

@@ -26,6 +26,7 @@ return {
         jsonc = { "prettierd", "prettier", stop_after_first = true },
         yaml = { "prettierd", "prettier", stop_after_first = true },
         markdown = { "prettierd", "prettier", stop_after_first = true },
+        mdx = { "prettierd", "prettier", stop_after_first = true },
         html = { "prettierd", "prettier", stop_after_first = true },
         css = { "prettierd", "prettier", stop_after_first = true },
         scss = { "prettierd", "prettier", stop_after_first = true },

modules/home/programs/nvim/lua/plugins/lsp.lua

@@ -101,6 +101,11 @@ return {
       lspconfig.clangd.setup({
         capabilities = capabilities,
       })
+
+      -- MDX
+      lspconfig.mdx_analyzer.setup({
+        capabilities = capabilities,
+      })
     end,
   },
 }

modules/home/programs/nvim/lua/plugins/treesitter.lua

@@ -27,6 +27,7 @@ return {
         "luap",
         "markdown",
         "markdown_inline",
+        "mdx",
         "nix",
         "norg",
         "printf",

packages/default.nix

@@ -4,8 +4,5 @@ let
   system = pkgs.stdenv.hostPlatform.system;
   llmPkgs = llm-agents.packages.${system};
 in {
-  osgrep = pkgs.callPackage ./osgrep.nix { };
   opencode = llmPkgs.opencode;
-  # Source beads from llm-agents.nix
-  beads = llmPkgs.beads;
 }

packages/osgrep.nix

@@ -1,32 +0,0 @@
-{ lib, buildNpmPackage, fetchurl, python3 }:
-
-buildNpmPackage rec {
-  pname = "osgrep";
-  version = "0.5.16";
-
-  src = fetchurl {
-    url = "https://registry.npmjs.org/${pname}/-/${pname}-${version}.tgz";
-    hash = "sha256-V23PNxtMCdRaqr4uDOs0rptmSROUrUO7I9HazoGqUCQ=";
-  };
-
-  sourceRoot = "package";
-
-  postPatch = ''
-    cp ${./osgrep-package-lock.json} package-lock.json
-  '';
-
-  npmDepsHash = "sha256-JDeZ3kcsbcZM//0846i1gsvoAgMpIpN8c160cp7wB5s=";
-
-  npmFlags = [ "--legacy-peer-deps" ];
-
-  dontNpmBuild = true; # Already built in npm package
-
-  nativeBuildInputs = [ python3 ];
-
-  meta = {
-    description = "Semantic grep for AI agents";
-    homepage = "https://github.com/Ryandonofrio3/osgrep";
-    license = lib.licenses.asl20;
-    mainProgram = "osgrep";
-  };
-}

shells/ai-agent.nix

@@ -1,56 +1,9 @@
 { pkgs, lib, customPkgs, ... }:
 
-let
+pkgs.mkShell {
-  # Get Beads package from custom packages
-  beadsPkg = customPkgs.beads;
-
-  # Helper script to show Beads project status
-  beadsStatus = pkgs.writeShellScriptBin "beads-status" ''
-    if [ ! -d ".beads" ]; then
-      echo "Not a Beads project (no .beads directory found)"
-      exit 1
-    fi
-
-    echo "=== Beads Project Status ==="
-    echo ""
-    echo "Ready tasks:"
-    ${beadsPkg}/bin/bd ready --json | ${pkgs.jq}/bin/jq -r '.[] | "  - [\(.id)] \(.title) (\(.type))"'
-    echo ""
-    echo "In Progress:"
-    ${beadsPkg}/bin/bd list --status in-progress --json | ${pkgs.jq}/bin/jq -r '.[] | "  - [\(.id)] \(.title)"'
-    echo ""
-    echo "For full details, run: bd list --json | jq"
-  '';
-
-  # Helper script to generate full project context for AI agents
-  beadsContext = pkgs.writeShellScriptBin "beads-context" ''
-    if [ ! -d ".beads" ]; then
-      echo "Not a Beads project (no .beads directory found)"
-      exit 1
-    fi
-
-    echo "=== Beads Project Context ==="
-    echo ""
-    echo "All issues:"
-    ${beadsPkg}/bin/bd list --json | ${pkgs.jq}/bin/jq '.'
-    echo ""
-    echo "Dependency tree (first ready task):"
-    ready_id=$(${beadsPkg}/bin/bd ready --json | ${pkgs.jq}/bin/jq -r '.[0].id // empty')
-    if [ -n "$ready_id" ]; then
-      ${beadsPkg}/bin/bd dep tree "$ready_id"
-    else
-      echo "No ready tasks"
-    fi
-  '';
-
-in pkgs.mkShell {
   name = "ai-agent";
 
   packages = with pkgs; [
-    # Custom packages
-    customPkgs.beads
-    customPkgs.osgrep
-
     # Version control
     git
     jujutsu
@@ -62,10 +15,6 @@ in pkgs.mkShell {
 
     # JSON processing
     jq
-
-    # Helper scripts
-    beadsStatus
-    beadsContext
   ];
 
   shellHook = ''
@@ -77,22 +26,7 @@ in pkgs.mkShell {
     echo "AI Agent development shell loaded"
     echo ""
     echo "Available tools:"
-    echo "  bd              - Beads CLI (issue tracker)"
-    echo "  beads-status    - Show project status summary"
-    echo "  beads-context   - Generate full context for AI"
-    echo "  osgrep          - Semantic code search"
     echo "  jj/git          - Version control"
     echo "  rg/ast-grep     - Code search"
-    echo ""
-    echo "Quick start:"
-    echo "  bd init         - Initialize Beads in current project"
-    echo "  bd create       - Create new issue"
-    echo "  bd ready        - Show ready tasks"
-    echo "  bd --help       - Full command reference"
-    echo ""
-    echo "Nushell helpers (if in nushell):"
-    echo "  bd-init         - Safe init with git checks"
-    echo "  bd-ready        - View ready tasks (structured)"
-    echo "  bd-sync         - Sync database with git"
   '';
 }