Xiki does what shell consoles do, but lets you edit everything at any time. It's trivial to make your own commands and menus to access other tools.
Donate to Xiki:
Type a word, any word. Then double click on it or type control-return (or command-return). For example type: git, bootstrap, mysql, mongo, rails, node, coffee, js, dom, jquery, svg, ruby code, file paths, url's, shell commands, etc.
Everything is editable text. Type commands anywhere. Edit the output. (Vs. typing commands at the bottom, and read-only output.) Intermix menus, headings, bullet points, wherever you want. Xiki == executable wiki.
Check out the screencast to see Xiki in action.
Create menus to access other tools just by typing. If the menu doesn't exist, xiki guides you through creating it.
Xiki merges shell and GUI concepts. Commands can have nested menus. Menus are just text indented by 2 spaces. Use the mouse or keyboard, whichever you prefer.