Claude Code is presented as a practical, step-by-step guide for developers to navigate, debug, refactor, test, and manage codebases for daily development tasks, including PR creation and session management. It emphasizes an interactive, conversational workflow within a terminal environment, leveraging natural language prompts for various code-related operations.

The core methodology of Claude Code revolves around an interactive, context-aware AI assistant that can:

1. Understand and Explore Codebases: Users can request high-level overviews of project structure, inquire about architectural patterns, data models, or authentication mechanisms. It allows for deep dives into specific components and tracing execution flows. The system recommends starting with broad questions and narrowing down, using project-specific terminology, and leveraging code intelligence plugins for "go to definition" and "find references" capabilities.
2. Debug and Fix Issues: Users share error messages, stack traces, and steps to reproduce problems. Claude Code can then suggest fixes, such as null checks, and apply them directly to files.
3. Refactor Code: It identifies deprecated API usage or recommends modern patterns for existing code. Users can prompt Claude to refactor code incrementally, ensuring backward compatibility and validating changes with tests.
4. Utilize Specialized Subagents: Claude Code supports the use of "subagents"—specialized AI entities designed to handle specific tasks more effectively (e.g., code-reviewer, debugger). These can be invoked automatically by Claude Code based on the task description or explicitly requested by the user. Users can list available subagents (/agents) and create custom ones by defining their purpose, activation conditions, tool access, and system prompts. Subagents can be shared across teams via .claude/agents/ directories.
5. Operate in Plan Mode: This is a read-only analysis mode designed for complex tasks like multi-step implementations, thorough code exploration, or safe code reviews. In Plan Mode, Claude uses a tool like AskUserQuestion to gather requirements and clarify goals before proposing a detailed plan. It can be activated during a session (Shift+Tab cycling through Normal, Auto-Accept, Plan modes), started directly with claude --permission-mode plan, or used in "headless" mode (-p) for single queries. Plans can be refined interactively, and users can edit proposed plans in their default text editor (Ctrl+G). Plan Mode can be set as a default permission mode in ~/.claude/settings.json.
6. Work with Tests: Claude Code identifies untested code, generates test scaffolding, adds meaningful test cases (including edge conditions), and runs/validates tests. It aims to generate tests adhering to the project's existing patterns, frameworks, and assertion styles by reviewing existing test files.
7. Create and Manage Pull Requests (PRs): Users can request summaries of their changes, create PRs directly (create a pr), or use the /commit-push-pr skill for a one-step commit, push, and PR creation. Claude Code integrates with Git, linking sessions to PRs (resumable via $claude --from-pr <number>$). PR descriptions can be enhanced collaboratively.
8. Handle Documentation: It identifies undocumented code, generates documentation (e.g., JSDoc comments), and refines it with context and examples, ensuring adherence to project standards.
9. Process Images: Users can drag-and-drop, paste, or provide paths to images. Claude Code can analyze image content (e.g., UI elements in screenshots, diagrams), use images for context (e.g., error screenshots, database schemas), and even generate code from visual inputs (e.g., CSS from mockups, HTML structure from components). It supports working with multiple images in a conversation.
10. Reference Files and Directories: The @ syntax allows users to quickly include the content of single files (e.g., @src/utils/auth.js) or list the structure of directories (e.g., @src/components) into the conversation, providing immediate context without waiting for Claude to discover them. It also supports referencing MCP (Management Control Plane) resources (e.g., @github:repos/owner/repo/issues).
11. Utilize Extended Thinking (Thinking Mode): This feature, active by default, enables Claude to perform multi-step internal reasoning before formulating a response. In verbose mode (Ctrl+O), users can observe this reasoning. With Opus 4.6, thinking is adaptive, dynamically allocating "thinking tokens" based on the user-selected "effort level" (low, medium, high), allowing for deeper analysis and self-correction. For other models, it uses a fixed token budget (default 31,999 tokens) which can be limited by MAX_THINKING_TOKENS. $MAX_THINKING_TOKENS=0$ disables thinking for all models.
12. Manage and Resume Sessions: Claude Code automatically saves conversation history. Users can resume previous sessions using claude --continue (most recent in current directory), claude --resume (interactive selector or by name), or $claude --from-pr <number>$. Sessions can be renamed (/rename) for easier identification. The interactive session selector allows filtering by current directory/all projects, git branch, and provides session metadata (name, last activity, message count, branch). Forked sessions (from /rewind or --fork-session) are grouped under their root.
13. Support Git Worktrees: This enables running parallel Claude Code sessions on isolated code copies within the same Git repository. Each worktree provides a separate working directory for a different branch or feature, ensuring complete code isolation for concurrent development tasks and dedicated Claude Code instances.
14. Function as a Unix-style Utility: Claude Code can be integrated into build scripts (e.g., package.json) for automated code review or linting. It supports piping data in (cat build-error.txt | claude -p '...') and piping structured output out, with options for text (default), json (JSON array of messages with metadata), or stream-json (real-time stream of JSON objects).
15. Self-Documentation: Claude has built-in access to its own documentation and can answer questions about its features, capabilities, limitations, and configurations (e.g., MCP integration, Amazon Bedrock).

The system architecture facilitates an agentic loop, managing context, and allowing for extensive configuration through settings.json, environment variables, and in-session commands, enabling a highly customizable and integrated development experience.