Permission Check

Purpose

Surface the full permission-mode picture across every layer Claude Code honors, so the user can see at a glance why prompts are (or aren't) firing. Claude Code resolves permission mode from a 6-tier stack; a single misconfigured layer produces silent overrides that are hard to debug by eye.

The 6 layers (precedence: bottom wins)

1. VSCode user settings — ~/Library/Application Support/Code/User/settings.json (macOS), %APPDATA%/Code/User/settings.json (Windows), ~/.config/Code/User/settings.json (Linux). Key: claudeCode.initialPermissionMode.
2. VSCode workspace settings — <repo>/.vscode/settings.json. Same key. Wins over user.
3. CLI user settings — ~/.claude/settings.json. Key: permissions.defaultMode.
4. CLI project settings — <repo>/.claude/settings.json. Same key. Wins over user.
5. CLI project-local settings — <repo>/.claude/settings.local.json. Same key. Wins over project.
6. In-session mode — set at session start from layers 1-5, then mutable via Shift+Tab (CLI) or the mode indicator (VS Code / Desktop); /permissions manages allow/deny rules, not the mode. Authoritative until session ends.

Two rules that override the stack (Anthropic's permission-modes docs, re-verified 2026-09-26):

• Layers 4 and 5 do not honor auto or bypassPermissions as a starting mode. A bypassPermissions there is ignored and the terminal session starts in Manual (default); an auto there is ignored in favour of the built-in default. Every other mode value applies from any layer.
• The VS Code extension does not read layers 4–5 for its starting mode; it uses claudeCode.initialPermissionMode (which does not accept auto), and a bypass value needs the extension's Allow dangerously skip permissions toggle. With no override, Claude Code ≥ 2.1.283 starts in auto mode.

So check first for "bypass set in the project settings, where it cannot take effect" — then for the mid-session override below.

Key insight: initialPermissionMode only fires at session start. If you toggled mid-session (or the session started before a settings change), the file-level settings are correct but the runtime mode differs. That, and a bypass set only in project settings, are the two usual sources of "bypass isn't working" confusion.

Privacy contract

Host-global settings files (~/.claude/settings.json, VSCode user settings) may contain:

• Paths to unrelated projects and secrets
• API keys, tokens, or provider credentials added outside this repo
• Permission policies set by the user's org or employer

This skill is designed for defense-in-depth: Phase A runs automatically and reads only repo-local files. Phase B reads host-global files only after the user explicitly confirms — never silently. When reporting host-global layers, redact any key that is not directly relevant to permissions.*, claudeCode.*, or allowDangerouslySkipPermissions.

Protocol

Phase A: Repo-local layers (auto-runs)

Read these immediately — they are checked into (or gitignored inside) the repo and do not cross the trust boundary:

VSCODE_WS="${CLAUDE_PROJECT_DIR}/.vscode/settings.json"
CLI_PROJECT="${CLAUDE_PROJECT_DIR}/.claude/settings.json"
CLI_LOCAL="${CLAUDE_PROJECT_DIR}/.claude/settings.local.json"

For each file that exists, extract:

• VSCode workspace: claudeCode.initialPermissionMode and allowDangerouslySkipPermissions (no claudeCode. prefix — flag the prefixed claudeCode.allowDangerouslySkipPermissions as a silently-ignored typo if you see it)
• CLI project / project-local: permissions.defaultMode, permissions.allow, permissions.deny

Missing files are fine — report "not present" rather than erroring.

Print the resolved defaultMode from these three layers alone, applying the two override rules above — a bypassPermissions or auto found only in layer 4 or 5 is reported as ignored, not as the resolved mode. If that already explains the prompt behavior (e.g. bypass set only in .claude/settings.json), stop here and surface the diagnosis with the fix: move it to ~/.claude/settings.json, pass --permission-mode bypassPermissions, or use auto mode.

Phase B: Host-global layers (requires explicit user confirmation)

If Phase A is inconclusive — e.g., all repo-local layers agree on bypass but the user is still being prompted — ask the user:

"To complete the diagnosis, I need to read two files outside this repo:

• ~/.claude/settings.json (CLI user-level)
• your VSCode user settings (~/Library/Application Support/Code/User/settings.json on macOS; Linux/Windows vary)

These may contain unrelated paths or secrets. I will redact any key that isn't in permissions.*, claudeCode.*, or allowDangerouslySkipPermissions. Proceed?"

Only after the user confirms, read:

# VSCode user (platform-dependent path; try all three)
case "$(uname -s)" in
    Darwin)  VSCODE_USER="${HOME}/Library/Application Support/Code/User/settings.json" ;;
    Linux)   VSCODE_USER="${HOME}/.config/Code/User/settings.json" ;;
    MINGW*|MSYS*|CYGWIN*) VSCODE_USER="${APPDATA}/Code/User/settings.json" ;;
    *)       VSCODE_USER="" ;;
esac

CLI_USER="${HOME}/.claude/settings.json"

When reporting their contents, extract only the relevant keys:

• CLI user: permissions.defaultMode, permissions.allow, permissions.deny
• VSCode user: any key starting with claudeCode.

Never print the full file. Redact everything else to (other keys redacted).

Step 2: Compute resolved state

The resolved defaultMode is the value from the highest-precedence layer that sets it. Report:

• Which layer won the defaultMode contest.
• Merged allow list (union across CLI tiers).
• Merged deny list (union; any deny blocks the action even if allowed elsewhere).
• Whether VSCode says bypass but CLI says otherwise (or vice versa) — this is a legitimate conflict to flag.

Step 3: Report runtime mode

The live in-session mode is exposed via the status line (see .claude/scripts/statusline.sh). Tell the user:

"If your status line shows a mode badge ([AUTO], [BYPASS], [PLAN], [AUTO-EDIT], [PROMPT]), that is the live in-session mode. If it disagrees with the resolved defaultMode above, either a mid-session toggle (Shift+Tab) changed it, or the resolution above already explains it — e.g. [PROMPT] from a bypass set only in project settings. No badge means Claude Code did not report the mode; the mode indicator in the Claude Code panel shows it."

If the status line isn't configured, emit a warning and point at .claude/scripts/statusline.sh.

Step 4: Flag common failure modes

Check for and explicitly call out:

1. Bypass or auto set only in project settings: layers 4–5 cannot set these starting modes. A bypass there starts the session in Manual; an auto there falls back to the built-in default (auto on ≥ 2.1.283). Fix: remove it from the project files and set bypass in user settings or with the CLI flag — or rely on the built-in auto default.
2. Layer drift: CLI user says bypass but CLI project-local says default → the project-local default wins (it is an honoured value), which explains the prompts.
3. VSCode-only bypass: VSCode layers say bypass but no CLI layer does → terminal Claude Code will still prompt; the extension honours it only with Allow dangerously skip permissions on.
4. Empty allowlist + default mode: defaultMode: "default" with empty allow → every tool prompts, as designed.
5. Stale session: settings are correct but user reports prompts → almost always a session that pre-dates the fix. Advise "Cmd+Shift+P → Developer: Reload Window, then new Claude Code session."
6. deny wins: any match in a deny list blocks the tool regardless of allow, in every mode including bypass — which is exactly why restricted-data projects use deny rules.

Output format

=== PERMISSION STATE ===

Layer 1 — VSCode user:       bypassPermissions      (allowDangerouslySkipPermissions: true)
Layer 2 — VSCode workspace:  (not set)
Layer 3 — CLI user:          bypassPermissions      (allow: ["*"])
Layer 4 — CLI project:       (not set)              (allow: ["Edit(**)", "Bash(*)", ...])
Layer 5 — CLI project-local: bypassPermissions      NOT HONOURED — a project-layer bypass starts the session in Manual

Resolved defaultMode: default (Manual) — Layer 5's bypass overrides Layer 3 and is not honoured
Merged allow:         Edit(**), Write(**), Bash(*), ...
Merged deny:          (none)

=== RUNTIME ===

Check the status line (or the mode indicator). Expected here: [PROMPT] — the ignored Layer 5 bypass explains it.
Remove the bypass from Layer 5 and keep it in Layer 3 (or rely on auto mode) to get [BYPASS] / [AUTO].
Any other mismatch with the resolved mode is an in-session override — Shift+Tab cycles modes.

=== DIAGNOSIS ===

No layer drift detected. If you are still seeing prompts:
  1. Session is stale (started before settings were applied) — reload window + new session.
  2. VSCode extension bug — check extension version and file an issue.
  3. Tool was previously denied in this session — that denial is remembered. New session clears it.

If any layer disagrees, replace the "No layer drift detected" line with a specific flagged issue.

Notes

• This skill is read-only. It never modifies settings.
• If $CLAUDE_PROJECT_DIR is unset, fall back to git rev-parse --show-toplevel.
• Platform-aware: detect macOS vs Linux vs Windows for the VSCode user path.