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/agents/agents.nix

@@ -8,15 +8,7 @@
   pkgs,
   videoDrivers ? [],
   ...
-}:
-with lib; let
-  npmGlobalPrefix = "${config.home.homeDirectory}/.npm-global";
-in {
-  home.file.".npmrc".text = ''
-    prefix=${npmGlobalPrefix}
-  '';
-  home.sessionVariables.NPM_CONFIG_PREFIX = npmGlobalPrefix;
-
+}: {
   imports = [
     # OpenCode and Pi agent configurations
     ./opencode.nix
@@ -70,35 +62,12 @@ in {
   home.packages = with pkgs; [
     agenix-cli
     agent-browser
-    alejandra
-    bc
-    bun
-    devpod
-    gnumake
-    cmake
-    (python3.withPackages (ps:
-      with ps; [
-        pip
-        uv
-        numba
-        numpy
-        torch
-        srt
-      ]))
     pyrefly
-    nixd
-    nix-update
-    nodejs
     (qmd.override {
       vulkanSupport = videoDrivers == ["amdgpu"];
       cudaSupport = videoDrivers == ["nvidia"];
     })
     openshell
     openspec
-    pi-coding-agent
-    sidecar
-    tailwindcss
-    tailwindcss-language-server
-    td
   ];
 }

home/coding/agents/pi.nix

@@ -41,7 +41,6 @@
         "npm:@plannotator/pi-extension"
         "npm:pi-powerline-footer"
         "npm:pi-markdown-preview"
-        "npm:pi-gsd"
         "npm:pi-tool-display"
         "npm:pi-agent-browser-native"
         "git:github.com/hk-vk/pi-connect"