CLI-based AI

Last updated on 2026-03-28 | Edit this page

Overview

Questions

  • Why use a CLI for AI instead of a browser?
  • What is the Living Spec and why does it matter?

Objectives

  • Compare CLI and browser-based AI tools.
  • Create a Living Spec (GEMINI.md) to guide an agent.
  • Explain the shift from writer to orchestrator.

Why CLI matters for research

Most researchers use chat-based AI in a browser. These tools are good for brainstorming but run in an isolated sandbox. They cannot see your files, run your code, or understand your project structure without manual uploads.

A CLI (Command Line Interface) agent runs in your terminal — the same place you run Python scripts or navigate your filesystem with ls and cd — and has access to three things a browser tool does not.

Your files and data. The agent can read your actual datasets, inspect your directory structure, and write scripts directly to disk. You are not copying and pasting between a chat window and a code editor. The agent works in your project the way a collaborator sitting at your machine would.

Your installed tools. Your machine probably has domain-specific software on it: geospatial tools like GDAL, bioinformatics pipelines, R packages, custom scripts, institutional data connectors. A browser AI has no idea these exist. A CLI agent can call them directly, pass output between them, and build on what you already have installed.

An iterative loop. When a script fails, the agent sees the error output in the terminal and can try again. You are not copying stack traces back into a chat window. The feedback loop is tight and stays in one place.

Caution

Data privacy and institutional context

The University of California and many other campuses have enterprise agreements with AI vendors like OpenAI and Google. These agreements usually state that your data will not be used to train public models.

However, CLI or API access under these agreements is not always documented. Campus IT often needs to provision this access, and terms can vary. Verify with your institution whether your license covers both web interfaces and CLI/API access.

Warning: Personal accounts may allow CLI/API usage but often lack the privacy protections of institutional licenses. Consult your campus IT policy before using AI tools with sensitive data.

Looking ahead: If your research requires absolute privacy, these skills transfer to open LLMs (like Gemma or Llama) run locally via Ollama.

Shift from writer to orchestrator

Traditional programming requires you to remember the syntax and logic of a script. Spec-Driven Research Orchestration offloads syntax generation to the AI, letting you focus on the high-level logic and the Living Spec.

graph TD
    A[Researcher] -->|Define goal| B(GEMINI.md\nLiving Spec)
    B --> C[Request a plan]
    C --> D{Approval Gate}
    D -->|Approve| E(AI Agent executes)
    D -->|Revise| C
    E -->|Draft code| F{Verification}
    F -->|Passed| G[Final Output]
    F -->|Failed| H[Refinement]
    H --> B
    style D fill:#bbf,stroke:#333,stroke-width:2px
    style F fill:#f9f,stroke:#333,stroke-width:2px

This introduces a new challenge: verification load. You must coordinate and validate the agent’s actions against your requirements.

Callout

Managing cognitive load

It is common to feel “out of the loop” when the AI generates many lines of code quickly. To manage this, focus on anchoring your understanding. Read the comments the AI generates and test small pieces of code frequently. If a block of logic is confusing, ask the AI to explain it before moving on.

File system access

Unlike browser tools, the Gemini CLI has access to your working environment. It can read project context from the directory structure and modify files. Instead of copying and pasting code, the agent writes scripts to your disk and can iterate based on terminal errors.

Caution

Security responsibility

Giving an AI agent access to your filesystem is a security responsibility. A buggy or misconfigured agent could delete files or access sensitive data, such as passwords.

Always consider that your tools can have unintended consequences. Ensure files are backed up or under version control (like Git) so you can revert unwanted changes.

Long context

Like humans, we only have a certain amount of working memory and LLMs operate in similar fashion. This is called the context window in LLM tools. Models like Gemini 2.5 have a long context window of 1 million to 2 million tokens. You can provide the AI with your entire project folder—scripts, documentation, and small datasets—at once.

This allows you to describe the desired state of your project, and the agent coordinates changes across multiple files. In a research context, this is declarative programming with AI agents.

Callout

A large context window is not a free pass

The more you load into a session, the more the model has to track. Beyond a certain point, quality degrades — the model may lose track of earlier instructions, produce inconsistent output, or fixate on the wrong files. This is sometimes called context poisoning.

A large context window makes this easier to run into, not harder. Managing what goes into your context is part of the workflow, not an afterthought.

Let’s make sure this works

Open a terminal window and type gemini --help and you should see something like:

BASH 

Usage: gemini [options] [command]

Gemini CLI - Defaults to interactive mode. Use -p/--prompt for non-interactive (headless) mode.

Commands:
  gemini [query..]             Launch Gemini CLI                                                                                                      [default]
  gemini mcp                   Manage MCP servers
  gemini extensions <command>  Manage Gemini CLI extensions.                                                                               [aliases: extension]
  gemini skills <command>      Manage agent skills.                                                                                            [aliases: skill]
  gemini hooks <command>       Manage Gemini CLI hooks.                                                                                         [aliases: hook]
...

Navigate to your project folder and start a session:

BASH 

cd /path/to/project/directory
gemini -p "Tell me what operating system I am currently using and list the files in this directory."

Compare the output to what you see when you run ls (or dir on Windows). Did the AI accurately describe your environment?

The AI should return a response similar to:

You are currently using macOS (Darwin). The files in this directory are:
- index.md
- config.yaml
- episodes/
- data/
...

Notice that gemini can ‘see’ your files and understands what environment you are working in.

We have a project folder that we want to start a project in, let’s initialize it as a gemini project and see what that does.

Callout

Working directory matters

Always start the Gemini CLI from inside your project folder. The agent uses the current directory to find your files and spec. Starting from the wrong folder — such as your home directory — is one of the most common sources of confusion in a workshop.

Initialize your project

The Gemini CLI includes an init command that creates a GEMINI.md template in your working directory:

BASH 

gemini

You are now inside Gemini. Press / to see the available slash commands and page through the full list. Notice /init — this is the command that will initialize our project. Let’s run it:

BASH 

/init

Notice that it does a bunch of stuff and inspects your file folders. After it finishes let’s see what new files have been created. You can do this inside gemini by:

BASH 

!ls

This shows the files that are created. You should see a file named GEMINI.md. Let’s look inside it using the cat command with !:

BASH 

!cat GEMINI.md

Here is what Gemini generated for a fresh empty project folder:

MARKDOWN 

# Project Context: vibe-coding-lesson

## Directory Overview

The `/Users/geno/Desktop/vibe-coding-lesson` directory appears to be an empty
project directory. It currently contains only this `GEMINI.md` file, which
serves as an index and context provider for the project.

## Key Files

*   **`GEMINI.md`**: This file contains project-specific context, documentation,
    and instructional information for AI agents and developers. It is intended to
    be updated as the project evolves.

## Usage

This directory is intended to be a workspace for the 'vibe-coding-lesson'
project. As it is currently empty, it is ready for initialization or the
addition of new files and code. Future usage will depend on the specific goals
of the 'vibe-coding-lesson' project.

---
*Last analyzed on: March 25, 2026*

A few things to notice. Gemini scanned the directory and described what it found. Because the folder was empty, it does not have much to say yet. Once you add data files, scripts, and documentation, running /init again will produce a richer spec that reflects your actual project. This is also something you will want to edit by hand — add your goals, constraints, and any rules you want the agent to follow.

The Living Spec

To get the most out of a CLI agent, provide it with persistent context about your project. This acts as a “Living Spec”—a set of rules and goals the agent must follow across every session.

Every major CLI tool has its own native spec file that it loads automatically when you start a session:

Tool Native spec file Auto-loaded?
Gemini CLI GEMINI.md Yes
Claude Code CLAUDE.md Yes
OpenAI Codex AGENTS.md Yes
Cursor .cursorrules Yes

You can also use a portable spec file—AGENTS.md is a common convention—that you explicitly reference in any prompt: "Read AGENTS.md and then...". It is not auto-loaded by any single tool, but it travels with your project if you switch tools. AGENTS.md was standardized in 2025 by the Agentic AI Foundation under the Linux Foundation — co-founded by Anthropic, OpenAI, and Block — making it the emerging cross-tool portable spec format.

What to include in your spec file

Use this file to define:

  • Current Goal: What you are working on right now.
  • Rules of the Road: Technical constraints (e.g., “Always use pandas for dataframes”).
  • Verification Gates: How you will confirm the code is correct.
Challenge

Challenge: Initialize and customize your spec file

Inside your Gemini CLI session, run /init to create a GEMINI.md file. Then open it in a text editor and add one “Hard Constraint” (something the AI must do) and one “Success Metric” (how you know it’s done).

MARKDOWN 

# Project: Arctic Sea Ice Analysis

## Goal
To analyze trends in sea ice extent from 1980-2020.

## Rules of the Road
- **Hard Constraint**: Only use the `xarray` library for spatial data processing.
- **Success Metric**: All final plots must include a valid DOI reference for the data source.

## Conventions
- Use snake_case for variable names.
- Save all plots to the `figures/` directory.
Key Points
  • CLI agents coordinate actions across multiple files.
  • Run /init inside Gemini to create a GEMINI.md Living Spec that reduces context drift.
  • A portable AGENTS.md lets the same spec travel across different AI tools.
  • Research orchestration shifts focus from writing syntax to validating intent.