sequant 2.2.0 → 2.4.0

package/dist/src/ui/tui/Header.d.ts

@@ -0,0 +1,6 @@
+import type { JSX } from "react";
+import type { RunSnapshot } from "../../lib/workflow/run-state.js";
+/** Top-of-dashboard summary: count, concurrency, base, quality-loop. */
+export declare function Header({ snapshot }: {
+    snapshot: RunSnapshot;
+}): JSX.Element;

package/dist/src/ui/tui/Header.js

@@ -0,0 +1,15 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Box, Text } from "ink";
+import { DIVIDER_COLOR } from "./theme.js";
+/** Top-of-dashboard summary: count, concurrency, base, quality-loop. */
+export function Header({ snapshot }) {
+    const { config, issues } = snapshot;
+    const concurrency = config.concurrency > 1
+        ? `parallel (${config.concurrency} concurrent)`
+        : "sequential";
+    const loop = config.qualityLoop ? "on" : "off";
+    const base = config.baseSha
+        ? `${config.baseBranch} @${config.baseSha.slice(0, 7)}`
+        : config.baseBranch;
+    return (_jsxs(Box, { flexDirection: "column", marginBottom: 1, children: [_jsxs(Box, { children: [_jsx(Text, { bold: true, children: "sequant run" }), _jsxs(Text, { color: DIVIDER_COLOR, children: ["  ─  ", issues.length, " issue", issues.length === 1 ? "" : "s", "  •  ", concurrency, "  •  ", "quality loop ", loop] })] }), _jsxs(Box, { children: [_jsx(Text, { color: DIVIDER_COLOR, children: "base " }), _jsx(Text, { children: base })] })] }));
+}

package/dist/src/ui/tui/IssueBox.d.ts

@@ -0,0 +1,16 @@
+import type { JSX } from "react";
+import type { IssueRuntimeState } from "../../lib/workflow/run-state.js";
+/**
+ * Three-cell rendering of a single issue's runtime state.
+ *
+ * Cells:
+ *   1. header  — id, title, phase N/total, elapsed
+ *   2. context — branch, phase progression, log path
+ *   3. activity — current `now` line, last-activity stamp
+ */
+export declare function IssueBox({ state, slot, width, now, }: {
+    state: IssueRuntimeState;
+    slot: number;
+    width: number;
+    now: number;
+}): JSX.Element;

package/dist/src/ui/tui/IssueBox.js

@@ -0,0 +1,68 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { Box, Text } from "ink";
+import { DIVIDER_COLOR, PHASE_GLYPHS, borderColorForIssue, phaseStatusColor, } from "./theme.js";
+import { Spinner } from "./Spinner.js";
+import { ElapsedTimer, formatSinceActivity } from "./ElapsedTimer.js";
+import { truncateToWidth } from "./truncate.js";
+/**
+ * Three-cell rendering of a single issue's runtime state.
+ *
+ * Cells:
+ *   1. header  — id, title, phase N/total, elapsed
+ *   2. context — branch, phase progression, log path
+ *   3. activity — current `now` line, last-activity stamp
+ */
+export function IssueBox({ state, slot, width, now, }) {
+    const border = borderColorForIssue(state.status, slot);
+    const innerWidth = Math.max(10, width - 4);
+    const doneCount = state.phases.filter((p) => p.status === "done" || p.status === "failed").length;
+    const activePhaseIndex = state.phases.findIndex((p) => p.status === "running");
+    const displayPhaseN = activePhaseIndex >= 0 ? activePhaseIndex + 1 : doneCount;
+    const total = state.phases.length;
+    const headerTitle = truncateToWidth(`#${state.number}  ${state.title}`, Math.max(10, innerWidth - 20));
+    return (_jsxs(Box, { flexDirection: "column", borderStyle: "round", borderColor: border, paddingX: 1, marginBottom: 1, width: width, children: [_jsxs(Box, { justifyContent: "space-between", children: [_jsx(Text, { color: border, children: headerTitle }), _jsxs(Text, { color: DIVIDER_COLOR, children: ["phase ", displayPhaseN, "/", total, " \u2022", " ", _jsx(ElapsedTimer, { startedAt: state.startedAt })] })] }), _jsx(Divider, { width: innerWidth, borderColor: border }), _jsxs(Box, { flexDirection: "column", children: [_jsxs(Box, { children: [_jsx(Text, { color: DIVIDER_COLOR, children: "branch " }), _jsx(Text, { children: truncateToWidth(state.branch, innerWidth - 8) })] }), _jsx(PhaseProgression, { phases: state.phases, borderColor: border }), state.currentPhase?.logPath ? (_jsxs(Box, { children: [_jsx(Text, { color: DIVIDER_COLOR, children: "log " }), _jsx(Text, { children: truncateToWidth(state.currentPhase.logPath, innerWidth - 8) })] })) : null] }), _jsx(Divider, { width: innerWidth, borderColor: border }), _jsx(Box, { flexDirection: "column", children: state.currentPhase ? (_jsxs(_Fragment, { children: [_jsxs(Box, { children: [_jsx(Text, { color: DIVIDER_COLOR, children: "now " }), _jsx(Spinner, { color: border }), _jsxs(Text, { children: ["  ", truncateToWidth(state.currentPhase.nowLine, innerWidth - 12)] })] }), _jsx(Box, { children: _jsxs(Text, { color: DIVIDER_COLOR, children: ["        └ last activity ", formatSinceActivity(now, state.currentPhase.lastActivityAt)] }) })] })) : (_jsx(Text, { color: DIVIDER_COLOR, children: statusLine(state) })) })] }));
+}
+function statusLine(state) {
+    switch (state.status) {
+        case "queued":
+            return "queued";
+        case "running":
+            return "working…";
+        case "passed":
+            return "completed";
+        case "failed":
+            return "failed";
+    }
+}
+function Divider({ width, borderColor, }) {
+    const mid = "─".repeat(Math.max(0, width - 2));
+    return (_jsxs(Text, { children: [_jsx(Text, { color: borderColor, children: "\u251C" }), _jsx(Text, { color: DIVIDER_COLOR, children: mid }), _jsx(Text, { color: borderColor, children: "\u2524" })] }));
+}
+function PhaseProgression({ phases, borderColor, }) {
+    return (_jsxs(Box, { flexWrap: "wrap", children: [_jsx(Text, { color: DIVIDER_COLOR, children: "phases " }), phases.map((p, i) => {
+                const isLast = i === phases.length - 1;
+                return (_jsxs(Box, { children: [_jsx(PhaseGlyph, { status: p.status, label: p.name, activeColor: borderColor, elapsedMs: p.elapsedMs }), !isLast ? (_jsxs(Text, { color: DIVIDER_COLOR, children: ["   ", PHASE_GLYPHS.separator, "   "] })) : null] }, `${p.name}-${i}`));
+            })] }));
+}
+function PhaseGlyph({ status, label, activeColor, elapsedMs, }) {
+    if (status === "running") {
+        return (_jsxs(Box, { children: [_jsx(Spinner, { color: activeColor }), _jsxs(Text, { children: [" ", label] })] }));
+    }
+    const glyph = status === "done"
+        ? PHASE_GLYPHS.done
+        : status === "failed"
+            ? PHASE_GLYPHS.failed
+            : PHASE_GLYPHS.pending;
+    const glyphColor = phaseStatusColor(status);
+    return (_jsxs(Box, { children: [_jsx(Text, { color: glyphColor, children: glyph }), _jsxs(Text, { color: DIVIDER_COLOR, children: [" ", label, elapsedMs != null ? ` ${formatShortDuration(elapsedMs)}` : ""] })] }));
+}
+function formatShortDuration(ms) {
+    const secs = Math.max(0, Math.floor(ms / 1000));
+    if (secs < 60)
+        return `${secs.toString().padStart(2, "0")}s`;
+    const mm = Math.floor(secs / 60)
+        .toString()
+        .padStart(2, "0");
+    const ss = (secs % 60).toString().padStart(2, "0");
+    return `${mm}:${ss}`;
+}

package/dist/src/ui/tui/Spinner.d.ts

@@ -0,0 +1,9 @@
+import { type JSX } from "react";
+import { type BorderColor } from "./theme.js";
+/**
+ * Braille spinner. Ticks at 10 Hz in its own component so the parent
+ * issue box is not forced to re-render on each frame.
+ */
+export declare function Spinner({ color }: {
+    color?: BorderColor;
+}): JSX.Element;

package/dist/src/ui/tui/Spinner.js

@@ -0,0 +1,18 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useEffect, useState } from "react";
+import { Text } from "ink";
+import { SPINNER_FRAMES } from "./theme.js";
+/**
+ * Braille spinner. Ticks at 10 Hz in its own component so the parent
+ * issue box is not forced to re-render on each frame.
+ */
+export function Spinner({ color }) {
+    const [frame, setFrame] = useState(0);
+    useEffect(() => {
+        const id = setInterval(() => {
+            setFrame((f) => (f + 1) % SPINNER_FRAMES.length);
+        }, 100);
+        return () => clearInterval(id);
+    }, []);
+    return _jsx(Text, { color: color, children: SPINNER_FRAMES[frame] });
+}

package/dist/src/ui/tui/index.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Experimental multi-issue TUI entry point.
+ *
+ * Mounts an `ink` app that polls `RunOrchestrator.getSnapshot()` at 10 Hz.
+ * Unmounts when the orchestrator reports `done` so the shell returns
+ * cleanly. Only safe to call when `process.stdout.isTTY` is true.
+ */
+import type { RunOrchestrator } from "../../lib/workflow/run-orchestrator.js";
+export interface TuiHandle {
+    /** Promise that resolves when the TUI unmounts. */
+    done: Promise<void>;
+    /** Force-unmount (e.g., on SIGINT fallback). */
+    unmount: () => void;
+}
+export declare function renderTui(orchestrator: RunOrchestrator): TuiHandle;

package/dist/src/ui/tui/index.js

@@ -0,0 +1,29 @@
+/**
+ * Experimental multi-issue TUI entry point.
+ *
+ * Mounts an `ink` app that polls `RunOrchestrator.getSnapshot()` at 10 Hz.
+ * Unmounts when the orchestrator reports `done` so the shell returns
+ * cleanly. Only safe to call when `process.stdout.isTTY` is true.
+ */
+import { createElement } from "react";
+import { render } from "ink";
+import { App } from "./App.js";
+export function renderTui(orchestrator) {
+    let resolveDone;
+    const done = new Promise((resolve) => {
+        resolveDone = resolve;
+    });
+    const instance = render(createElement(App, {
+        getSnapshot: () => orchestrator.getSnapshot(),
+        onDone: () => {
+            instance.unmount();
+        },
+    }), { exitOnCtrlC: false });
+    instance.waitUntilExit().then(() => resolveDone());
+    return {
+        done,
+        unmount: () => {
+            instance.unmount();
+        },
+    };
+}

package/dist/src/ui/tui/theme.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Theme tokens for the experimental multi-issue dashboard TUI.
+ *
+ * Palette rotates by start order (cyan → magenta → blue → yellow); issue
+ * status (failed / passed) overrides the rotation color where applicable.
+ * Respects `NO_COLOR` automatically via `ink`/`chalk`.
+ */
+import type { IssueStatus, PhaseStatus } from "../../lib/workflow/run-state.js";
+/** Border-color palette rotated by issue start order. */
+export declare const BORDER_ROTATION: readonly ["cyan", "magenta", "blue", "yellow"];
+export type BorderColor = (typeof BORDER_ROTATION)[number] | "green" | "red" | "gray";
+/** Gray used for horizontal dividers inside each box. */
+export declare const DIVIDER_COLOR: "gray";
+/**
+ * Pick the border color for an issue.
+ * Failed / passed states win over rotation; otherwise rotate by slot.
+ */
+export declare function borderColorForIssue(status: IssueStatus, slot: number): BorderColor;
+/** Glyphs for the phase progression row. */
+export declare const PHASE_GLYPHS: {
+    readonly pending: "○";
+    readonly done: "✓";
+    readonly failed: "✗";
+    readonly separator: "▸";
+};
+/** Braille spinner frames — 10 Hz rotation looks smooth at ~100ms tick. */
+export declare const SPINNER_FRAMES: readonly ["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
+/** Color for a phase glyph based on its status. Active phase uses border color. */
+export declare function phaseStatusColor(status: PhaseStatus): BorderColor;

package/dist/src/ui/tui/theme.js

@@ -0,0 +1,52 @@
+/**
+ * Theme tokens for the experimental multi-issue dashboard TUI.
+ *
+ * Palette rotates by start order (cyan → magenta → blue → yellow); issue
+ * status (failed / passed) overrides the rotation color where applicable.
+ * Respects `NO_COLOR` automatically via `ink`/`chalk`.
+ */
+/** Border-color palette rotated by issue start order. */
+export const BORDER_ROTATION = ["cyan", "magenta", "blue", "yellow"];
+/** Gray used for horizontal dividers inside each box. */
+export const DIVIDER_COLOR = "gray";
+/**
+ * Pick the border color for an issue.
+ * Failed / passed states win over rotation; otherwise rotate by slot.
+ */
+export function borderColorForIssue(status, slot) {
+    if (status === "failed")
+        return "red";
+    if (status === "passed")
+        return "green";
+    const idx = ((slot % BORDER_ROTATION.length) + BORDER_ROTATION.length) %
+        BORDER_ROTATION.length;
+    return BORDER_ROTATION[idx];
+}
+/** Glyphs for the phase progression row. */
+export const PHASE_GLYPHS = {
+    pending: "○",
+    done: "✓",
+    failed: "✗",
+    separator: "▸",
+};
+/** Braille spinner frames — 10 Hz rotation looks smooth at ~100ms tick. */
+export const SPINNER_FRAMES = [
+    "⠋",
+    "⠙",
+    "⠹",
+    "⠸",
+    "⠼",
+    "⠴",
+    "⠦",
+    "⠧",
+    "⠇",
+    "⠏",
+];
+/** Color for a phase glyph based on its status. Active phase uses border color. */
+export function phaseStatusColor(status) {
+    if (status === "done")
+        return "green";
+    if (status === "failed")
+        return "red";
+    return "gray";
+}

package/dist/src/ui/tui/truncate.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Display-width-aware truncation for terminal output.
+ *
+ * Uses `string-width` so wide glyphs (CJK, emoji) and ANSI escapes are
+ * counted correctly. Cheaper than ink's own truncation in hot paths.
+ */
+/**
+ * Truncate `text` so its visible width does not exceed `max` columns.
+ * If truncation happens, appends a single `…` (which itself counts as 1 col).
+ */
+export declare function truncateToWidth(text: string, max: number): string;

package/dist/src/ui/tui/truncate.js

@@ -0,0 +1,31 @@
+/**
+ * Display-width-aware truncation for terminal output.
+ *
+ * Uses `string-width` so wide glyphs (CJK, emoji) and ANSI escapes are
+ * counted correctly. Cheaper than ink's own truncation in hot paths.
+ */
+import stringWidth from "string-width";
+/**
+ * Truncate `text` so its visible width does not exceed `max` columns.
+ * If truncation happens, appends a single `…` (which itself counts as 1 col).
+ */
+export function truncateToWidth(text, max) {
+    if (max <= 0)
+        return "";
+    const width = stringWidth(text);
+    if (width <= max)
+        return text;
+    if (max === 1)
+        return "…";
+    let acc = "";
+    let accWidth = 0;
+    const budget = max - 1; // reserve one column for the ellipsis
+    for (const ch of text) {
+        const w = stringWidth(ch);
+        if (accWidth + w > budget)
+            break;
+        acc += ch;
+        accWidth += w;
+    }
+    return `${acc}…`;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "sequant",
-  "version": "2.2.0",
+  "version": "2.4.0",
   "description": "Quantize your development workflow - Sequential AI phases with quality gates",
   "type": "module",
   "bin": {
@@ -26,7 +26,9 @@
     "test": "vitest run",
     "lint": "eslint src/ bin/ --max-warnings 0",
     "sync:skills": "cp -r templates/skills/* .claude/skills/",
+    "sync:hooks": "bash scripts/sync-hooks.sh",
     "validate:skills": "for skill in templates/skills/*/; do npx skills-ref validate \"$skill\"; done",
+    "lint:skill-calls": "npx tsx scripts/lint-skill-calls.ts",
     "prepare:marketplace": "npx tsx scripts/prepare-marketplace.ts",
     "validate:marketplace": "npx tsx scripts/prepare-marketplace.ts --validate-only",
     "prepublishOnly": "npm run build"
@@ -64,7 +66,7 @@
   },
   "homepage": "https://sequant.io",
   "engines": {
-    "node": ">=20.19.0"
+    "node": ">=22.12.0"
   },
   "peerDependencies": {
     "@modelcontextprotocol/sdk": "^1.27.1"
@@ -75,20 +77,24 @@
     }
   },
   "dependencies": {
-    "@anthropic-ai/claude-agent-sdk": "^0.2.11",
-    "@hono/node-server": "^1.19.9",
+    "@anthropic-ai/claude-agent-sdk": "^0.3.142",
+    "@hono/node-server": "^2.0.0",
     "boxen": "^8.0.1",
     "chalk": "^5.3.0",
     "chokidar": "^5.0.0",
     "cli-table3": "^0.6.5",
     "commander": "^14.0.3",
-    "diff": "^8.0.3",
+    "diff": "^9.0.0",
     "gradient-string": "^3.0.0",
     "hono": "^4.12.1",
-    "inquirer": "^13.3.0",
+    "ink": "^7.0.1",
+    "inquirer": "^14.0.1",
+    "log-update": "^7.0.1",
     "open": "^11.0.0",
     "ora": "^9.3.0",
     "p-limit": "^7.3.0",
+    "react": "^19.2.5",
+    "string-width": "^8.2.0",
     "yaml": "^2.7.0",
     "zod": "^4.3.5"
   },
@@ -97,10 +103,12 @@
     "@types/gradient-string": "^1.1.6",
     "@types/inquirer": "^9.0.7",
     "@types/node": "^25.4.0",
+    "@types/react": "^19.2.14",
     "@typescript-eslint/eslint-plugin": "^8.58.0",
     "@typescript-eslint/parser": "^8.58.0",
     "eslint": "^10.1.0",
     "globals": "^17.0.0",
+    "ink-testing-library": "^4.0.0",
     "tsx": "^4.19.2",
     "typescript": "^6.0.2",
     "typescript-eslint": "^8.58.0",

package/templates/agents/sequant-explorer.md

@@ -1,6 +1,7 @@
 ---
 name: sequant-explorer
 description: Codebase exploration agent for sequant /spec phase. Searches for existing patterns, components, database schemas, and file structures. Use when gathering context before planning a feature implementation.
+# Note: per anthropics/claude-code#43869 this is currently a no-op; agent runs on parent's model
 model: haiku
 maxTurns: 15
 tools:

package/templates/agents/sequant-qa-checker.md

@@ -1,7 +1,8 @@
 ---
 name: sequant-qa-checker
 description: Quality check agent for sequant /qa phase. Runs type safety, scope/size, security, and documentation checks on diffs. Use when spawned by the /qa skill to perform parallel or sequential quality checks.
-model: haiku
+# Note: per anthropics/claude-code#43869 this is currently a no-op; agent runs on parent's model
+model: sonnet
 permissionMode: bypassPermissions
 effort: low
 maxTurns: 15

package/templates/agents/sequant-testgen.md

@@ -1,6 +1,7 @@
 ---
 name: sequant-testgen
 description: Test stub generator for sequant /testgen phase. Parses verification criteria from /spec comments and generates Jest/Vitest test stubs with Given/When/Then structure. Use when spawned by the /testgen skill.
+# Note: per anthropics/claude-code#43869 this is currently a no-op; agent runs on parent's model
 model: haiku
 maxTurns: 25
 tools:

package/templates/hooks/post-tool.sh

@@ -13,6 +13,17 @@ if [[ "${CLAUDE_HOOKS_DISABLED:-}" == "true" ]]; then
     exit 0
 fi
 
+# === RELAY CHECK (#383) ===
+# Sourced only when SEQUANT_RELAY=true. The check itself is a single env-var
+# comparison when relay is disabled (default), so non-relay runs incur no cost.
+if [[ "${SEQUANT_RELAY:-}" == "true" ]]; then
+    _RELAY_CHECK="$(dirname "${BASH_SOURCE[0]:-$0}")/relay-check.sh"
+    if [[ -f "${_RELAY_CHECK}" ]]; then
+        # shellcheck source=relay-check.sh disable=SC1091
+        source "${_RELAY_CHECK}" || true
+    fi
+fi
+
 # === READ INPUT FROM STDIN ===
 # Claude Code passes tool data as JSON via stdin, not environment variables
 INPUT_JSON=$(cat)
@@ -216,6 +227,60 @@ if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE '(npm run build
     fi
 fi
 
+# === TEST COVERAGE ANALYSIS (P3) ===
+# Opt-in: Set CLAUDE_HOOKS_COVERAGE=true to enable
+# Automatically appends coverage analysis to npm test output
+# Logs which changed files have/don't have corresponding tests
+if [[ "${CLAUDE_HOOKS_COVERAGE:-}" == "true" ]]; then
+    if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE '(npm (test|run test)|bun (test|run test)|yarn (test|run test)|pnpm (test|run test))'; then
+        # Only run if tests passed (don't clutter failure output)
+        if ! echo "$TOOL_OUTPUT" | grep -qE '(FAIL|failed|Error:)'; then
+            COVERAGE_LOG="${_LOG_DIR}/claude-coverage.log"
+
+            # Get changed source files (excluding tests)
+            changed_files=$(git diff main...HEAD --name-only 2>/dev/null | grep -E '\.(ts|tsx|js|jsx)$' | grep -v -E '\.test\.|\.spec\.|__tests__' || true)
+
+            if [[ -n "$changed_files" ]]; then
+                echo "$(date +%H:%M:%S) COVERAGE_ANALYSIS: Checking test coverage for changed files" >> "$QUALITY_LOG"
+
+                files_with_tests=0
+                files_without_tests=0
+                critical_without_tests=""
+
+                while IFS= read -r file; do
+                    [[ -z "$file" ]] && continue
+                    base=$(basename "$file" .ts | sed 's/\.tsx$//')
+
+                    # Check for test file
+                    if find . -name "${base}.test.*" -o -name "${base}.spec.*" 2>/dev/null | grep -q .; then
+                        ((files_with_tests++))
+                    else
+                        ((files_without_tests++))
+                        # Check if critical path
+                        if echo "$file" | grep -qE 'auth|payment|security|server-action|middleware|admin'; then
+                            critical_without_tests="$critical_without_tests $file"
+                        fi
+                    fi
+                done <<< "$changed_files"
+
+                total=$((files_with_tests + files_without_tests))
+
+                # Log coverage summary
+                echo "$(date +%H:%M:%S) COVERAGE: $files_with_tests/$total changed files have tests" >> "$COVERAGE_LOG"
+
+                if [[ -n "$critical_without_tests" ]]; then
+                    echo "$(date +%H:%M:%S) ⚠️ CRITICAL_NO_TESTS:$critical_without_tests" >> "$COVERAGE_LOG"
+                    echo "$(date +%H:%M:%S) CRITICAL_NO_TESTS:$critical_without_tests" >> "$QUALITY_LOG"
+                fi
+
+                if [[ $files_without_tests -gt 0 ]]; then
+                    echo "$(date +%H:%M:%S) COVERAGE_GAP: $files_without_tests files without tests" >> "$QUALITY_LOG"
+                fi
+            fi
+        fi
+    fi
+fi
+
 # === SMART TEST RUNNING (P3) ===
 # Opt-in: Set CLAUDE_HOOKS_SMART_TESTS=true to enable
 # Runs related tests asynchronously after file edits
@@ -300,4 +365,31 @@ if [[ -n "${CLAUDE_HOOKS_WEBHOOK_URL:-}" ]]; then
     fi
 fi
 
+# === POST-MERGE WORKTREE CLEANUP ===
+# Clean up worktree AFTER `gh pr merge` succeeds (not before).
+# Previous approach removed worktree pre-merge, which lost work if merge failed.
+if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE 'gh pr merge'; then
+    # Only clean up if merge succeeded (output contains merge confirmation)
+    if echo "$TOOL_OUTPUT" | grep -qiE '(merged|Merged pull request|Pull request .* merged)'; then
+        PR_NUM=$(echo "$TOOL_INPUT" | grep -oE 'gh pr merge [0-9]+' | grep -oE '[0-9]+')
+
+        if [[ -n "$PR_NUM" ]]; then
+            BRANCH_NAME=$(gh pr view "$PR_NUM" --json headRefName --jq '.headRefName' 2>/dev/null || true)
+
+            if [[ -n "$BRANCH_NAME" ]]; then
+                # Note: worktree line is 2 lines before branch line in porcelain output
+                WORKTREE_PATH=$(git worktree list --porcelain 2>/dev/null | grep -B2 "branch refs/heads/$BRANCH_NAME" | grep "^worktree " | sed 's/^worktree //' || true)
+
+                if [[ -n "$WORKTREE_PATH" && -d "$WORKTREE_PATH" ]]; then
+                    git worktree remove "$WORKTREE_PATH" --force 2>/dev/null || true
+                    echo "POST-MERGE: Removed worktree $WORKTREE_PATH for branch $BRANCH_NAME" >> "${_LOG_DIR}/claude-hook.log"
+                fi
+
+                # Clean up local branch
+                git branch -D "$BRANCH_NAME" 2>/dev/null || true
+            fi
+        fi
+    fi
+fi
+
 exit 0

package/templates/hooks/pre-tool.sh

@@ -104,20 +104,23 @@ if echo "$TOOL_INPUT" | grep -qE '^(env|printenv|export)$'; then
 fi
 
 # Destructive system commands
-if echo "$TOOL_INPUT" | grep -qE 'sudo|rm -rf /|rm -rf ~|rm -rf \$HOME'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#570)
+if ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'sudo|rm -rf /|rm -rf ~|rm -rf \$HOME'; then
     echo "HOOK_BLOCKED: Destructive system command" | tee -a "$HOOK_LOG" >&2
     exit 2
 fi
 
 # Deployment (should never happen in issue automation)
-if echo "$TOOL_INPUT" | grep -qE 'vercel (deploy|--prod)|terraform (apply|destroy)|kubectl (apply|delete)'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#570)
+if ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'vercel (deploy|--prod)|terraform (apply|destroy)|kubectl (apply|delete)'; then
     echo "HOOK_BLOCKED: Deployment command" | tee -a "$HOOK_LOG" >&2
     exit 2
 fi
 
 # Force push
 # Pattern requires -f to be a standalone flag (not part of branch name like -fix)
-if echo "$TOOL_INPUT" | grep -qE 'git push.*(--force| -f($| ))'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#564)
+if ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'git push.*(--force| -f($| ))'; then
     echo "HOOK_BLOCKED: Force push" | tee -a "$HOOK_LOG" >&2
     exit 2
 fi
@@ -127,7 +130,8 @@ fi
 # - Unpushed commits on main/master
 # - Uncommitted changes (staged or unstaged)
 # - Unfinished merge in progress
-if echo "$TOOL_INPUT" | grep -qE 'git reset.*(--hard|origin)'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#570)
+if ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'git reset.*(--hard|origin)'; then
     CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo "")
     BLOCK_REASONS=""
     
@@ -167,7 +171,8 @@ if echo "$TOOL_INPUT" | grep -qE 'git reset.*(--hard|origin)'; then
 fi
 
 # CI/CD triggers (automation shouldn't trigger more automation)
-if echo "$TOOL_INPUT" | grep -qE 'gh workflow run'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#570)
+if ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'gh workflow run'; then
     echo "HOOK_BLOCKED: Workflow trigger" | tee -a "$HOOK_LOG" >&2
     exit 2
 fi
@@ -225,7 +230,8 @@ check_sensitive_files() {
 
 if [[ "${CLAUDE_HOOKS_SECURITY:-true}" != "false" ]]; then
     # Security checks for git commit
-    if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
+    # Skip for gh issue/pr commands — body text may legitimately reference these tokens (#564)
+    if [[ "$TOOL_NAME" == "Bash" ]] && ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
         # Skip security checks if --no-verify is used
         if ! echo "$TOOL_INPUT" | grep -qE -- '--no-verify'; then
             # Check staged files for secrets
@@ -257,7 +263,8 @@ fi
 # --- No-Changes Guard (AC-7) ---
 # Block commits when there are no staged or unstaged changes (prevents empty commits)
 # Skips for --amend since amending doesn't require new changes
-if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#564)
+if [[ "$TOOL_NAME" == "Bash" ]] && ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
     if ! echo "$TOOL_INPUT" | grep -qE -- '--amend|--allow-empty'; then
         # Extract target directory from cd command if present (for worktree commits)
         # Handles: "cd /path && git commit" or "cd /path; git commit"
@@ -284,7 +291,8 @@ fi
 # Warn (but don't block) when committing outside a feature worktree
 # This catches accidental commits to main repo during feature work
 QUALITY_LOG="${_LOG_DIR}/claude-quality.log"
-if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#564)
+if [[ "$TOOL_NAME" == "Bash" ]] && ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
     CWD=$(pwd)
     if ! echo "$CWD" | grep -qE 'worktrees/feature/'; then
         echo "$(date +%H:%M:%S) WORKTREE_WARNING: Committing outside feature worktree ($CWD)" >> "$QUALITY_LOG"
@@ -295,7 +303,8 @@ fi
 # --- Commit Message Validation (AC-3) ---
 # Enforce conventional commits format: type(scope): description
 # Types: feat|fix|docs|style|refactor|test|chore|ci|build|perf
-if [[ "$TOOL_NAME" == "Bash" ]] && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
+# Skip for gh issue/pr commands — body text may legitimately reference these tokens (#564)
+if [[ "$TOOL_NAME" == "Bash" ]] && ! echo "$TOOL_INPUT" | grep -qE '^gh (issue|pr) ' && echo "$TOOL_INPUT" | grep -qE 'git commit'; then
     # Extract message from -m flag
     MSG=""