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/base/cli-tools/packages.nix

@@ -22,22 +22,30 @@ in {
       jq
       ripgrep
 
+      # Nix
+      alejandra
+      comma
+      nixd
+      nix-diff
+      nix-index
+      nix-update
+
       # Dev tools
+      bc
+      cmake
       devenv
       gcc
+      gnumake
       go
       httpie
       just
       lazygit
-      nix-index
-      nix-update
       progress
       sqlite
       sqlite-vec
       tldr
 
       # AI tools
-      comma
       fabric-ai
       llm