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
+  ];
+}