I prefer CLI tools during development because the tools tend to be simpler ("rougher") and easier to compose into pipelines. If you aren't using your tools this way, you're missing out on a lot of what makes them useful. They also are a lot easier to script and write documentation for...type this, type this, type this--okay, according to your shell history, you didn't type what we told you to and there's your problem.
GUI tools are useful for when I'm debugging graphical issues in the frontend (what is the DOM looking like starting under the cursor right now?), or need to very rapidly switch context in the backend (what are these variables set to? What is the prototype and doc for this function invocation?). They are annoying to script, and annoying to document for other developers. They also tend to be much larger and less composable than other tools.
As far as the git stuff, well, it's best used from the command-line.
