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Claude Code Operation

Configure and operate Claude Code for a team: know where instructions, skills, commands, subagents and memory live; how the CLAUDE.md and settings hierarchies resolve; and how to run sessions, headless and streaming modes, and permission modes safely.

Key points

1
Core components: CLAUDE.md files and .claude/rules/ hold standing instructions. Skills (SKILL.md) are reusable procedures, invoked as /name or loaded automatically when their description matches. Subagents (.claude/agents/, ~/.claude/agents/) run in their own context windows. Hooks give deterministic automation. Auto memory holds notes Claude keeps for itself.
2
Custom commands have been merged into skills. .claude/commands/deploy.md and .claude/skills/deploy/SKILL.md both create /deploy; skills add supporting files and automatic invocation. $ARGUMENTS (or $0, $1, and so on) inserts the text typed after the command.
3
CLAUDE.md scopes: managed policy (for example /etc/claude-code/CLAUDE.md on Linux) for the whole organization; ~/.claude/CLAUDE.md for you in every project; ./CLAUDE.md or ./.claude/CLAUDE.md for the team, committed; ./CLAUDE.local.md for you in this project, gitignored.
4
CLAUDE.md files in the working directory and its parents load at launch and are concatenated, not overridden. Files in subdirectories load on demand when Claude reads files there. @path imports still load at launch, so they organize content without saving context. Keep each file under about 200 lines.
5
Rules: .md files in .claude/rules/ load unconditionally unless they have paths frontmatter (globs), in which case they load only when Claude works with matching files. ~/.claude/rules/ holds personal rules for all projects.
6
Repository initialization: /init analyzes the codebase and generates a starting CLAUDE.md (build and test commands, conventions). If one exists, it suggests improvements instead of overwriting. Then add what Claude cannot discover on its own.
7
Auto memory is on by default and machine-local: notes live in ~/.claude/projects/<project>/memory/, with a MEMORY.md index loaded at session start. It is not shared with teammates, so team conventions belong in the project CLAUDE.md. Manage it with /memory.
8
Subagent persistent memory (the memory frontmatter field) has three scopes: user (~/.claude/agent-memory/, all projects), project (.claude/agent-memory/, shareable through git) and local (.claude/agent-memory-local/, not committed).
9
settings.json precedence, highest first: managed settings, command-line arguments, .claude/settings.local.json, .claude/settings.json, ~/.claude/settings.json. Nothing a developer sets overrides managed settings. Array settings such as permissions.allow merge across scopes.
10
Sessions: claude --continue (-c) reopens the most recent conversation in the current directory. claude --resume (-r) reopens a specific session by ID or name, or shows a picker. --fork-session resumes under a new session ID. In scripts with overlapping runs, capture session_id from JSON output and use --resume.
11
Headless mode: claude -p "..." runs once and exits. --output-format is text, json (one final object with result, session_id and cost) or stream-json (newline-delimited events). --json-schema with json returns structured_output. Use --allowedTools to pre-approve tools and --bare for fast, reproducible scripted runs.
12
Streaming mode: --output-format stream-json --verbose --include-partial-messages streams token deltas, and the last line is a result message. --input-format stream-json accepts streamed input.
13
Permission modes: default (Manual), acceptEdits (file edits and common filesystem commands), plan (read-only analysis), auto (acts without prompts while background safety checks screen actions), dontAsk (only pre-approved actions; everything else is denied, suited to CI) and bypassPermissions (no checks; isolated containers or VMs only). Shift+Tab cycles modes.
14
Auto mode treats boundaries you state in chat ("don't push") as block signals, but these live in the transcript and can be lost to compaction. For a hard guarantee, add a deny rule; deny rules apply in every mode. Admins can turn auto mode off with disableAutoMode in managed settings.

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