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/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))
+    ];
+  };
+}