A practical guide to Claude Code configuration in 2025

Claude Code is a seriously impressive agentic coding assistant that lives right in your terminal. If you haven't tried it, it feels a lot like having a senior developer pair-programming with you, ready to help 24/7. But here's the thing: its real strength is unlocked through a flexible, and let's be honest, pretty complex configuration system. Most people just scratch the surface, which means they're missing out on what makes it so special.

This guide is here to walk you through everything you need to know about your Claude Code configuration. We'll start with the basics and work our way up to advanced integrations. The goal is to show you how to tailor it to your exact workflow and, just as importantly, to help you see its limits so you know when you might need a different kind of tool to tackle bigger business challenges.

What is Claude Code?

At its heart, Claude Code is an AI coding assistant from Anthropic that you run from your command line. You can think of it as a version of Claude that's been specifically fine-tuned to understand and work within your local development environment. Its whole purpose is to help with the day-to-day grind of being a developer: analyzing code, building new features, squashing bugs, and writing tests.

It does this by getting its hands dirty, so to speak. Claude Code can read and write files directly in your project, run shell commands to execute scripts or check your git status, and even integrate with external tools to pull in more context. It’s a tool built by developers, for developers, designed to live and breathe inside your codebases.

Understanding the core Claude Code configuration

To really make Claude Code feel like your assistant, you need to

Claude Code has been running flawlessly for me by literally telling it to come up with a plan to make a change. For example: 'Think of a way to create a custom contact page for this website. Think of any potential roadblocks and or errors that may occur'. Then, I just take that output and paste it into Gemini, and tell it 'Here is my plan to create a custom contact page for my website: [plan would go here]' (If you want to make it even better give it access to your code). Tell it to critique and make changes to this plan. Then you just feed the critiques back into Claude code and they go back and forth for a while until they both settle on a plan that sounds good. Now you just tell Claude code 'Implement the plan, make sure to check for errors as you go' and I have done this about 13 times and it has built and deployed, no extra debugging.

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Using CLAUDE.md for project context

Think of "CLAUDE.md" as Claude's long-term memory for your project. It's a simple Markdown file that the AI reads automatically every time you start a session. This is where you tell it about your project's specific rules, coding standards, and common commands so you don't have to repeat yourself in every single prompt.

Here are a few examples of what you might put in a "CLAUDE.md" file:

• Coding style guidelines: "Use TypeScript for all new code and follow the existing ESLint configuration."

• Testing instructions: "Write tests for all new functions using Jest. Place them alongside the source files with a ".test.ts" extension."

• Architectural overview: "The frontend is a Next.js app, the backend is Node.js with Express, and we use PostgreSQL with Prisma for the database."

You can put these files in your project's root directory to share them with your team, or in your home folder ("~/.claude/CLAUDE.md") for global instructions that apply to all your projects. This layering lets you build up a rich, persistent context for the AI.

Programmatic control with settings.json

While "CLAUDE.md" handles the "what" and "why," "settings.json" is all about the "how." This is where you configure Claude Code's technical behavior, like its permissions, which AI model to use, and how it interacts with your system.

Here are some of the key settings you can adjust:

• "model": You can specify which Claude model you want to use, like "claude-opus-4-1-20250805" for maximum power or "claude-sonnet-4-5-20250929" for a balance of speed and intelligence.

• "permissions": This one is huge for security. You can define what tools Claude is allowed to use without asking, like "allow: ["Read(./src/**)", "Bash(git *)"]", and what it's absolutely forbidden from doing, like "deny: ["Read(./.env)"]".

• "hooks": You can set up automations that trigger based on Claude's actions. For example, you could create a hook to automatically run a code formatter like Prettier every time Claude writes to a JavaScript file.

The configuration hierarchy explained

Claude Code has a clear pecking order for applying settings, which gives you a ton of control. Settings at a higher level will always override those at a lower level. This means you can set enterprise-wide security policies that can't be bypassed, while still letting individual developers customize their personal workflows.

The hierarchy looks like this, from highest priority to lowest:

1. Enterprise Policies: Top-level rules, often for security and compliance.

2. Command-Line Flags: Temporary overrides for a single session.

3. Local Project Settings (".claude/settings.local.json"): Personal preferences for a specific project that you don't commit to git.

4. Shared Project Settings (".claude/settings.json"): Team-wide settings that are checked into version control.

5. Global User Settings ("~/.claude/settings.json"): Your personal defaults for all projects.

Extending Claude Code with tools and integrations

Out of the box, Claude Code is smart, but its real magic comes from its ability to interact with your developer environment and connect to external services.

Managing built-in tool permissions

Claude Code comes with some powerful built-in tools like "Bash", "Read", "Write", "Edit", and "WebFetch". For your own safety, it asks for permission before it does anything that could change your system, like editing a file or running a command.

This is great for preventing accidents, but it can slow you down if you're constantly typing "yes" to approve the same safe actions. You can use the "/permissions" command in a session or edit your "settings.json" file to create an "allowlist" for commands you trust. For example, you could tell it to always allow "git commit" commands but continue to ask for permission before running something riskier like "rm -rf".

Adding advanced capabilities with MCP servers

MCP, or Model Context Protocol, is a system that lets Claude Code connect to external tools and services, massively extending what it can do. It's basically a plugin system that gives Claude new skills.

With the right MCP servers, you can enable Claude to:

• Connect directly to your company's database to query live data.

• Integrate with project management tools like Jira to create tickets or update issue statuses.

• Use specialized scientific research tools for data analysis, like those found in ToolUniverse.

Setting up MCP servers is definitely a power-user feature, usually done through the "claude mcp add" command or by manually editing your configuration files. But it opens up a world of possibilities for automating some really complex, multi-step workflows.

Practical Claude Code configuration workflows and when to use a different tool

Now that we've covered how to set up your Claude Code configuration, let's talk about why you'd use it in your daily work, and maybe more importantly, what its limits are.

Common developer workflows

Once you've got it configured just right, you can build some seriously effective workflows. Here are a few common ones:

• Test-Driven Development: Start by asking Claude to write a set of failing tests for a new feature. Once they're written and you've confirmed they fail, you can then tell it to write the code that makes them all pass.

• Codebase Onboarding: When you're new to a project, you can use Claude as a Q&A tool to get up to speed. Ask it high-level questions like, "How does authentication work in this project?" and it will search the code to give you a detailed breakdown.

• Automated Refactoring: Give Claude a class or module and ask it to refactor it based on specific principles. For instance, "Refactor this service to use dependency injection and make it more testable."

This video provides a complete guide to Claude Code, covering best practices, strategies, and tips for various configurations and workflows.

The limitations: When code isn't your only knowledge source

Here’s the thing to remember: Claude Code is built for developers working with code. But what happens when the information needed to solve a problem isn't in a code file? What if the answer is buried in past Zendesk tickets, scattered across Confluence pages, or hidden in old Slack conversations?

That's where Claude Code hits a wall. It isn't designed to connect all those different business knowledge sources. It can't learn from your past customer interactions or your internal documentation to help with tasks like customer support or answering questions for your internal team.

This is exactly where a platform like eesel AI shines. It’s built from the ground up to connect all of your company's knowledge, no matter where it lives.

• Get up and running in minutes: Unlike the developer-focused setup of Claude Code, eesel AI is completely self-serve. You can connect it to your tools with a few clicks and have an AI agent working in minutes, not months.

• Unify all your knowledge: It instantly connects to your helpdesks, wikis, and documents. It can learn from thousands of your past support tickets automatically to understand your brand voice and common solutions right from the start.

Claude Code pricing and plans

You don't buy Claude Code as a standalone product; it's bundled with Anthropic's other offerings. You can use it if you have a Claude Pro or Max subscription, or you can pay as you go through the Anthropic API.

Here's a simple breakdown of the official pricing:

It's worth noting that this pricing is based on usage and tokens, which can get unpredictable and expensive for high-volume tasks like automating customer support. This is a key difference from eesel AI's predictable plans, which have no per-resolution fees. You don't have to worry about a surprise bill after a busy month.

The right tool for the right job

Claude Code is an incredibly capable and highly configurable tool that can genuinely improve a developer's workflow. Taking the time to master its configuration is how you unlock its full potential, turning it from a simple assistant into a true collaborator.

But it’s a specialized tool for a specialized job: coding. Its greatest strengths are its deep integration with a developer's local environment and its ability to understand and manipulate code.

When your goal shifts from writing code to automating business processes like customer support, internal IT helpdesks, or company-wide Q&A, you need a tool that's built for that universe. If you're looking to connect your business knowledge from helpdesks, wikis, and other documents to power autonomous AI agents, it might be time to explore a solution designed for that challenge.

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