Cf init

CLI Usage: When unsure about a CLI's interface or flags, run it with --help first. Do NOT attempt to discover functionality by reading plugin source code — doing so leads to incorrect execution from assumptions made without context of the holistic flow.

Initialize CLEAR Framework

Set up CLEAR (Context Layered Engineering for Agentic Resources) in the current project. This skill runs a single CLI command that creates the .clear/ directory structure, generates a project manifest, initializes Session 0, configures hooks, configures the statusline, and returns a structured JSON result. Claude then adds session resume instructions to CLAUDE.md.

Plugin Root Resolution

CLI commands in this skill reference $CLEAR_PLUGIN_ROOT — a .claude/settings.json env var the shell expands. The SessionStart hook persists it, but settings env vars load at session launch, so on a brand-new consumer's first session (before its next restart) the variable is empty and node "$CLEAR_PLUGIN_ROOT/build/..." fails with MODULE_NOT_FOUND. This matters most for /cf-init, which a consumer always runs before any restart.

First-session bootstrap — if $CLEAR_PLUGIN_ROOT is empty, set it inline in the same Bash call as the CLI (each Bash call is a fresh shell, so a separate export would not carry over):

export CLEAR_PLUGIN_ROOT="${CLEAR_PLUGIN_ROOT:-${CLAUDE_PLUGIN_ROOT}}"

Prepend it to the CLI in one shell line: export CLEAR_PLUGIN_ROOT="${CLEAR_PLUGIN_ROOT:-${CLAUDE_PLUGIN_ROOT}}"; <node "$CLEAR_PLUGIN_ROOT/build/..." command>. ${CLAUDE_PLUGIN_ROOT} resolves in this SKILL.md body to the actually-loaded plugin path; once the consumer restarts, $CLEAR_PLUGIN_ROOT is populated and the assignment is a harmless no-op.

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When to Use This Skill

Trigger Pattern	Example User Request	Flag
First-time CLEAR setup	"Initialize CLEAR in this project"	(none)
Reinitialize from scratch (DESTRUCTIVE)	"Reset CLEAR — start fresh", "Reinitialize CLEAR"	--reinit-clean
Refresh meta files only (non-destructive)	"Refresh my CLAUDE.md from the latest CLEAR template", "Update CLEAR rules.md"	--refresh-config
Set up framework tracking	"Set up CLEAR so my sessions are tracked"	(none)

Destructiveness matrix:

Flag	What it does	What it preserves
(none)	First-time init — refuses if .clear/ already exists	n/a
--reinit-clean	Creates a .clear.backup.<ts>/ then DELETES .clear/ (knowledge, workpackages, sessions, audit). Re-initializes Session 0.	Nothing inside .clear/. Backup directory only.
--refresh-config	Rewrites ONLY CLAUDE.md + .claude/rules/rules.md from latest CLEAR templates. Idempotent.	All of .clear/. All sessions/knowledge/workpackages untouched.
--force	DEPRECATED alias for --reinit-clean. Will be removed in CLEAR vNEXT. Emits stderr warning.	Same as --reinit-clean.

DO NOT use for:

• Checking CLEAR status after initialization (use /cf-status instead)
• Reloading configuration without reinitializing (use /cf-reload instead)

Recommendation logic (BINDING):

If the user asks to "refresh", "update", "re-sync", or "reload" CLEAR meta files (CLAUDE.md or rules.md) and their stated goal is NOT to wipe existing knowledge/sessions/workpackages, recommend --refresh-config and explicitly warn against --reinit-clean/--force. The destructive flags wipe ALL .clear/ state with no shipped restore CLI in Phase A — recovery requires manual copy from the timestamped backup directory.

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Mandatory Execution Checklist (BINDING)

Every item below is mandatory. Execute in order. No skipping.

• Pre-flight check completed (determine initialization state)
• Init CLI executed (creates .clear/ structure, manifest, config, session 0, env vars, statusline)
• CLI output parsed and verified (success / partial / error)
• Session resume instructions added to project CLAUDE.md
• Success output displayed with project ID, session ID, and next steps

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Command Reference

Init CLI at $CLEAR_PLUGIN_ROOT/build/infrastructure/init/cli/.

Pre-init note on the plugin root: $CLEAR_PLUGIN_ROOT is persisted into the project's .claude/settings.json by the SessionStart hook on the first session after initialization. On a brand-new project it is therefore empty until cf-init has run and Claude Code has been restarted — so on the very first /cf-init, $CLEAR_PLUGIN_ROOT may be blank. When it is, use Claude Code's native per-plugin variable $CLAUDE_PLUGIN_ROOT as the --plugin-root value (and in the CLI path) instead. After the first post-init restart, $CLEAR_PLUGIN_ROOT is set and the table commands below work as written.

Action	CLI Command
Initialize CLEAR	init-cli --cwd=. --plugin-root=$CLEAR_PLUGIN_ROOT
Reinitialize from scratch (DESTRUCTIVE)	init-cli --cwd=. --plugin-root=$CLEAR_PLUGIN_ROOT --reinit-clean
Refresh meta files only (non-destructive)	init-cli --cwd=. --plugin-root=$CLEAR_PLUGIN_ROOT --refresh-config
Reinitialize (legacy alias)	init-cli --cwd=. --plugin-root=$CLEAR_PLUGIN_ROOT --force ← DEPRECATED

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Usage

/cf-init [--reinit-clean | --refresh-config | --force]

Arguments:

• --reinit-clean — DESTRUCTIVE. Creates a timestamped backup at .clear.backup.<ts>/, then DELETES the existing .clear/ directory (knowledge, workpackages, sessions, audit). Re-initializes a fresh .clear/ with Session 0. Use when intentionally starting over.
• --refresh-config — Non-destructive. Rewrites ONLY CLAUDE.md and .claude/rules/rules.md from the latest CLEAR templates. Leaves .clear/ entirely untouched. Idempotent — re-running on an up-to-date project is a no-op. Use when you only want to pick up new CLEAR governance text.
• --force — DEPRECATED alias for --reinit-clean. Same destructive behavior; emits a stderr deprecation warning. Will be removed in CLEAR vNEXT.

Current arguments: $ARGUMENTS

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Instructions

Pre-flight Check

Before any initialization, determine the current state and intent:

ls -la .clear/config/clear-manifest.yaml 2>/dev/null && echo "ALREADY_INITIALIZED" || echo "NOT_INITIALIZED"

Branch on result:

• ALREADY_INITIALIZED + no flag: Display a message explaining the project is already initialized. Surface the three options to the user:
  • --refresh-config to rewrite only CLAUDE.md + rules.md from latest templates (non-destructive).
  • --reinit-clean to wipe .clear/ and start over (DESTRUCTIVE — creates a backup but deletes all knowledge/sessions/workpackages).
  • Do nothing if neither matches their intent. STOP here.
• .clear/ exists but no manifest: Display an error explaining this is an unknown state that cannot be safely initialized. STOP here.
• NOT_INITIALIZED: Proceed with the init CLI below (no destructive-flag prompt needed).
• ALREADY_INITIALIZED + --reinit-clean or --force: Execute the Destructiveness Confirmation Prompt below BEFORE running the CLI.
• ALREADY_INITIALIZED + --refresh-config: Proceed directly to the init CLI (non-destructive path; no confirmation needed).

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Destructiveness Confirmation Prompt (BINDING — --reinit-clean / --force only)

If the user invoked /cf-init --reinit-clean or /cf-init --force against an already-initialized project, emit the following warning to the user BEFORE running the CLI and pause for explicit confirmation:

WARNING — --reinit-clean is destructive.

Running this will create a backup at .clear.backup.<ts>/, then DELETE the existing .clear/ directory. You will lose:

• All knowledge entries
• All workpackages
• All session handoffs
• The audit log

Phase A of WP-PS1 does not yet ship a restore CLI. Recovery requires manually copying files back from the backup directory.

If your goal is to refresh CLAUDE.md or .claude/rules/rules.md only, use /cf-init --refresh-config instead — it leaves .clear/ entirely untouched.

Confirm: do you want to proceed with the destructive reinit? (yes/no)

• If the user answers yes: proceed to the init CLI.
• If the user answers no (or anything other than yes): STOP. Do not run the CLI. Suggest --refresh-config if their goal is meta-refresh.

If the user invoked --force, ALSO mention that --force is deprecated and --reinit-clean is the new name.

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Run Init CLI

Execute the init CLI to perform .clear/ setup. The argument list depends on which flag the user passed:

# Determine the flag arg to pass through
FLAG_ARG=""
case "$ARGUMENTS" in
  --reinit-clean) FLAG_ARG="--reinit-clean" ;;
  --refresh-config) FLAG_ARG="--refresh-config" ;;
  --force) FLAG_ARG="--force" ;;
esac

node "$CLEAR_PLUGIN_ROOT/build/infrastructure/init/cli/init-cli.js" \
  --cwd="$PROJECT_DIR" \
  --plugin-root="$CLEAR_PLUGIN_ROOT" \
  $FLAG_ARG

For --refresh-config (non-destructive path): the CLI invokes ONLY updateProjectClaudeMd + updateProjectRulesMd. None of the directory/manifest/session/hook/statusline steps run. Output JSON will have status: "success" with no init block.

For full init / --reinit-clean / --force: the CLI performs:

1. (Force path only) Creates .clear.backup.<ts>/ backup, deletes existing .clear/
2. Creates .clear/ directory structure (7 subdirectories)
3. Creates manifest at .clear/config/clear-manifest.yaml
4. Creates configuration at .clear/config/clear-config.yaml
5. Initializes Session 0 (session.json, session-history.json, sync-state.json)
6. Configures environment variables (kill switches) in .claude/settings.json
7. Configures statusline for context window detection in .claude/settings.json

Do NOT use Write or Edit on any .clear/ file. The CLI handles all .clear/ mutations via fs.writeFileSync, which is invisible to the PreToolUse guard.

Parse CLI Output

The CLI returns JSON:

{
  "status": "success | partial | error",
  "init": {
    "success": true,
    "projectName": "...",
    "projectPath": "...",
    "projectId": "prj-xxxxxxxx",
    "sessionId": "init-xxxx-...",
    "steps": [{"step": "...", "success": true}],
    "checks": [{"name": "...", "passed": true, "message": "..."}]
  },
  "statusline": {
    "needsRestart": true,
    "originalStatusline": null
  },
  "error": "..." 
}

Branch on status:

• success + init block present: Full init succeeded. Proceed to Step 6.
• success + NO init block: --refresh-config path completed (non-destructive meta-file refresh). CLAUDE.md + .claude/rules/rules.md are now updated. Step 6 (session-resume append) is NOT needed — skip it. Report completion to the user and STOP.
• partial: Init succeeded but statusline configuration failed. Proceed to Step 6 with a warning about statusline.
• error: Initialization failed. Display the error message and the init.steps array showing which steps completed. Advise the user to run /cf-init --reinit-clean to retry. If the error is CONFLICTING_FLAGS, explain that --refresh-config cannot be combined with --reinit-clean or --force.

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Add Session Resume Instructions (Step 6)

This is the only Write operation in the skill — it writes to CLAUDE.md, NOT to .clear/.

Append session resume instructions to the project's CLAUDE.md file. These instructions tell Claude how to restore CLEAR context after /clear or compaction events. If CLAUDE.md does not exist, create it with the resume instructions.

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Error Recovery

If initialization fails partway through:

• Report which steps completed successfully (from init.steps array)
• Report which step failed and the reason
• Provide guidance:
  • First-time init failure → "Run /cf-init again to retry."
  • Reinit failure (partial wipe) → "Run /cf-init --reinit-clean to retry from scratch. A backup of the prior state was created at .clear.backup.<ts>/."
  • CONFLICTING_FLAGS error → "--refresh-config and --reinit-clean/--force are mutually exclusive. Pick one based on intent."

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Completion Checklist

For first-time init or --reinit-clean / --force:

• (If reinit) Destructiveness Confirmation Prompt presented to user and explicit "yes" received before running the CLI
• (If --force) User informed that --force is deprecated and --reinit-clean is the new name
• Init CLI executed successfully (or partially with statusline warning)
• .clear/ directory contains all 7 subdirectories (verified by CLI steps)
• Configuration and manifest files exist (verified by CLI)
• Session 0 is active (verified by CLI)
• Environment variables configured (verified by CLI)
• Session resume instructions appended to CLAUDE.md
• Success output displayed: project ID, Session 0 ID, and next steps
• User informed of next steps: create a plan, define workpackages, run /cf-status
• If statusline was configured (statusline.needsRestart is true): "Please exit and restart Claude Code. After restarting, the CLEAR statusline appears at the bottom of the screen — that confirms it is working. If it is missing or you want to verify the install wiring, run /cf-debug install."
• Context advisory displayed: "CLEAR calculates context based on max usage, but it is advisable to start a new session after hitting 75%+ of operational context."

For --refresh-config:

• Init CLI executed successfully with status: "success" and no init block in output
• User informed: "CLAUDE.md and .claude/rules/rules.md refreshed from latest CLEAR templates. .clear/ was not touched — all sessions, knowledge, and workpackages remain intact."
• Step 6 (session-resume append) intentionally SKIPPED — the CLI's update already handles meta-file content.