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/default.nix

@@ -1,11 +1,12 @@
 # Coding environment aggregator — profile-independent development tooling.
-# Imports editors, LSP servers, git configuration, the agent system, and optional packages.
+# Imports editors, LSP servers, git configuration, the agent system, language runtimes, and optional packages.
 {...}: {
   imports = [
     ./editor
     ./lsp
     ./git/git.nix
     ./agents/agents.nix
+    ./languages
     ./packages.nix
   ];
 }