Quick Reference: Domain 3 — Claude Code Configuration & Workflows

CLAUDE.md files are concatenated into context, not overridden. Every applicable file loads together, in a documented order from broadest scope to most specific:

Key rule: This is a load order, not a precedence chain — no file replaces another. If two rules contradict each other, Claude may pick one arbitrarily, so fix contradictions at the source. Distractors claiming "more specific scope wins" or "user-level overrides project-level" are wrong.

Files in .claude/rules/ use YAML frontmatter with a paths field for conditional loading:

---
paths:
  - "src/api/**"
  - "src/middleware/**"
---
Always validate authentication tokens before processing API requests.
Use structured error responses with proper HTTP status codes.

Rules are loaded only when Claude Code operates on files matching the glob patterns. This prevents irrelevant rules from consuming context window space.

Skill properties:

• allowed-tools — The exam guide describes this as restricting the skill's tool access, and that is the expected exam answer. In current Claude Code (July 2026) it pre-approves the listed tools so they run without a permission prompt; disallowed-tools and permission deny rules do the restricting
• context: fork — Runs in a forked context so skill execution does not pollute the main conversation

Skills are reusable capability modules. They encapsulate a workflow (e.g., "run tests", "deploy to staging") with tool access configured in frontmatter.

Commands are invoked with / prefix. They are templates — predefined prompts that can include $ARGUMENTS placeholders for user input.

Difference from skills: Commands and skills have been merged into one system — both create /commands. A command is a single flat .md file (a prompt template, $ARGUMENTS supported); a skill is a directory with a SKILL.md entrypoint that adds supporting files, frontmatter configuration, and automatic invocation when relevant.

Critical property: Hooks are deterministic — they run as code, not as model instructions. They cannot be bypassed by prompt injection or model reasoning.

Contrast with prompt instructions:

• Prompt: "Never delete production files" → Probabilistic, may be violated
• PreToolUse hook blocking rm on /prod/ paths → Deterministic, cannot be violated

Plan mode signals: The task is complex, has multiple valid approaches, or the consequences of a wrong approach are high. Plan mode forces Claude to outline its approach before executing.

-p flag: Runs Claude Code in non-interactive mode. Essential for CI/CD integration. No confirmation prompts, no interactive input — the command must be self-contained.

-p is the most-tested flag, but know the rest of the headless toolkit too.

System prompt — append vs replace (exam favourite):

The *-file variants (--append-system-prompt-file, --system-prompt-file) load the same text from a file.

• Concrete examples beat prose descriptions. Show the code you want, not a paragraph describing it.
• Batch interacting fixes in a single message so the model sees all the constraints at once. Fix independent issues sequentially, one focused change at a time.
• Independent review sessions: Never review code in the same session that wrote it. The model retains reasoning bias from the writing session. Start a fresh session for review.
• Severity calibration: Use examples to show what constitutes a critical issue vs. a minor style nit. Without calibration, the model treats all issues as equally important.

• Permissions are controlled at the tool level — you grant or deny access to specific tools.
• A subagent's tool set is scoped with the tools field on its AgentDefinition; skills use allowed-tools frontmatter (see Skills System above).
• Principle of least privilege: Each agent/skill should have access only to the tools it needs.
• Project-level settings (.claude/) are committed and shared. Personal settings (~/.claude/) are not.