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/agents/pi.nix

@@ -41,7 +41,6 @@
         "npm:@plannotator/pi-extension"
         "npm:pi-powerline-footer"
         "npm:pi-markdown-preview"
-        "npm:pi-gsd"
         "npm:pi-tool-display"
         "npm:pi-agent-browser-native"
         "git:github.com/hk-vk/pi-connect"