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/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;
+  };
+}