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/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
+    ];
+  };
+}