refactor: add language runtimes module and cleanup agent config

- Add home/coding/languages/ with Python, JavaScript, Rust, Go, TypeScript
- Move bun/nodejs from agents.nix to languages/javascript.nix
- Move python3 with packages to languages/python.nix
- Move npm config to javascript.nix (broader context)
- Add language options to m3-ares and m3-kratos host configs
- Move pyrefly from agents.nix to lsp/servers.nix
- Remove duplicate python3 reference (build conflict fix)
- Remove unused base/secrets/cli-tools/ duplicates

home/coding/languages/default.nix

@@ -0,0 +1,10 @@
+# Language runtimes — Python, JavaScript, Rust, Go, TypeScript.
+{...}: {
+  imports = [
+    ./python.nix
+    ./javascript.nix
+    ./rust-toolchain.nix
+    ./go.nix
+    ./typescript.nix
+  ];
+}

home/coding/languages/go.nix

@@ -0,0 +1,19 @@
+# Go toolchain — compiler and language server.
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+with lib; let
+  cfg = config.coding.languages.go;
+in {
+  options.coding.languages.go.enable = mkEnableOption "Go toolchain";
+
+  config = mkIf cfg.enable {
+    home.packages = with pkgs; [
+      go
+      gopls
+    ];
+  };
+}

home/coding/languages/javascript.nix

@@ -0,0 +1,25 @@
+# JavaScript/TypeScript runtime — Node.js and Bun.
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+with lib; let
+  cfg = config.coding.languages.javascript;
+  npmGlobalPrefix = "${config.home.homeDirectory}/.npm-global";
+in {
+  options.coding.languages.javascript.enable = mkEnableOption "JavaScript runtime (Node.js + Bun)";
+
+  config = mkIf cfg.enable {
+    home.packages = with pkgs; [
+      nodejs
+      bun
+    ];
+
+    home.file.".npmrc".text = ''
+      prefix=${npmGlobalPrefix}
+    '';
+    home.sessionVariables.NPM_CONFIG_PREFIX = npmGlobalPrefix;
+  };
+}

home/coding/languages/python.nix

@@ -0,0 +1,30 @@
+# Python runtime with pip and uv.
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+with lib; let
+  cfg = config.coding.languages.python;
+in {
+  options.coding.languages.python = {
+    enable = mkEnableOption "Python runtime with pip and uv";
+    extraPackages = mkOption {
+      type = types.listOf types.package;
+      default = [];
+      example = literalExpression "[ pkgs.python3Packages.numpy ]";
+      description = "Additional Python packages to include";
+    };
+  };
+
+  config = mkIf cfg.enable {
+    home.packages = [
+      (pkgs.python3.withPackages (ps:
+        with ps; [
+          pip
+          uv
+        ] ++ cfg.extraPackages))
+    ];
+  };
+}

home/coding/languages/rust-toolchain.nix

@@ -0,0 +1,20 @@
+# Rust toolchain — compiler, package manager, and language server.
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+with lib; let
+  cfg = config.coding.languages.rustToolchain;
+in {
+  options.coding.languages.rustToolchain.enable = mkEnableOption "Rust toolchain";
+
+  config = mkIf cfg.enable {
+    home.packages = with pkgs; [
+      rustc
+      cargo
+      rust-analyzer
+    ];
+  };
+}

home/coding/languages/typescript.nix

@@ -0,0 +1,19 @@
+# TypeScript support — language server and type checking tools.
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+with lib; let
+  cfg = config.coding.languages.typescript;
+in {
+  options.coding.languages.typescript.enable = mkEnableOption "TypeScript support";
+
+  config = mkIf cfg.enable {
+    home.packages = with pkgs; [
+      typescript
+      typescript-language-server
+    ];
+  };
+}