@boyingliu01/xp-gate 0.29.0 → 0.30.1

package/gate-3.sh

@@ -77,7 +77,24 @@ else
     
     # Get changed source files for complexity check (includes test files)
     CC_FILES=$(echo "$CHANGED_FILES" | grep -E '\.(ts|tsx|js|jsx|py|go|java|swift|cpp|c|hpp|h|m|mm|kt)$' || true)
-    
+
+    # Grade exactly the population the baseline was written from. The two must
+    # match or the ratchet reports pre-existing code as "new", which is a false
+    # BLOCK no repair can clear (the exact failure #495 Round 3 called out, in a
+    # different place). scripts/ccn-report.cjs --write-baseline records only
+    # bucket === 'production' rows; its bucketFor() classifies two other buckets:
+    #   mirror     src/npm-package/**, plugins/*/src/** — regenerated by prepack
+    #              from a canonical source that IS graded here. Editing a mirror
+    #              is reverted at the next publish, so grading it cannot be acted
+    #              on (doctorDelphi CCN=106 blocked every src/npm-package commit,
+    #              on HEAD too — no baseline entry could ever exist for it).
+    #   test       __tests__/, *.test.*, *_test.{py,go}, *Test(s).java — recorded
+    #              in the report's test bucket, never in the baseline.
+    # Both prefixes and the test pattern mirror ccn-report.cjs so the gate and
+    # the writer cannot drift apart again (pinned by __tests__/gate-3-*.bats).
+    CC_FILES=$(echo "$CC_FILES" | grep -vE \
+      '^"?src/npm-package/|^"?plugins/[^/]+/src/|(^|/)__tests__?/|\.test\.[cm]?[jt]sx?$|_test\.(py|go)$|Test(s)?\.java$' || true)
+
     if [ -n "$CC_FILES" ]; then
       echo "Checking complexity for source files..."
       

package/hooks/gate-3.sh

@@ -77,7 +77,24 @@ else
     
     # Get changed source files for complexity check (includes test files)
     CC_FILES=$(echo "$CHANGED_FILES" | grep -E '\.(ts|tsx|js|jsx|py|go|java|swift|cpp|c|hpp|h|m|mm|kt)$' || true)
-    
+
+    # Grade exactly the population the baseline was written from. The two must
+    # match or the ratchet reports pre-existing code as "new", which is a false
+    # BLOCK no repair can clear (the exact failure #495 Round 3 called out, in a
+    # different place). scripts/ccn-report.cjs --write-baseline records only
+    # bucket === 'production' rows; its bucketFor() classifies two other buckets:
+    #   mirror     src/npm-package/**, plugins/*/src/** — regenerated by prepack
+    #              from a canonical source that IS graded here. Editing a mirror
+    #              is reverted at the next publish, so grading it cannot be acted
+    #              on (doctorDelphi CCN=106 blocked every src/npm-package commit,
+    #              on HEAD too — no baseline entry could ever exist for it).
+    #   test       __tests__/, *.test.*, *_test.{py,go}, *Test(s).java — recorded
+    #              in the report's test bucket, never in the baseline.
+    # Both prefixes and the test pattern mirror ccn-report.cjs so the gate and
+    # the writer cannot drift apart again (pinned by __tests__/gate-3-*.bats).
+    CC_FILES=$(echo "$CC_FILES" | grep -vE \
+      '^"?src/npm-package/|^"?plugins/[^/]+/src/|(^|/)__tests__?/|\.test\.[cm]?[jt]sx?$|_test\.(py|go)$|Test(s)?\.java$' || true)
+
     if [ -n "$CC_FILES" ]; then
       echo "Checking complexity for source files..."
       

package/hooks/hook-module-resolution.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+# GENERATED FILE — DO NOT EDIT.
+# Source of truth: src/npm-package/lib/hook-module-resolution.js
+# Regenerate: node scripts/generate-hook-resolution.cjs
+#
+# The module resolution order (#505) lives in one place, as data. This file
+# is its shell projection. Editing it by hand makes the hook disagree with
+# doctor.js, which reads the JS module directly — the exact divergence
+# #495/#500 were about.
+
+# Probe file used to pick the gate tier.
+HOOK_GATE_PROBE="gate-3.sh"
+
+# ADAPTER_DIR cascade, highest priority first.
+# Each entry is "tier_id|base_var|probe_file".
+HOOK_ADAPTER_DIR_TIERS=(
+  'global|GLOBAL_ADAPTER_DIR|adapter-common.sh'
+  'project|PROJECT_GITHOOKS|adapter-common.sh'
+  'script|SCRIPT_DIR|adapter-common.sh'
+)
+
+# Adapter resolution tiers, highest priority first.
+# Each entry is "tier_id|base_var|template" with {name} as the basename.
+HOOK_ADAPTER_TIERS=(
+  'adapter_flat|ADAPTER_DIR|{name}.sh'
+  'adapter_nested|ADAPTER_DIR|adapters/{name}.sh'
+  'project_nested|PROJECT_GITHOOKS|adapters/{name}.sh'
+  'script_nested|SCRIPT_DIR|adapters/{name}.sh'
+)
+
+# Gate resolution tiers, highest priority first.
+# Semantics differ from adapter tiers: each entry names the DIRECTORY that
+# would hold the gate probe, so a match yields the directory (GATE_DIR), not
+# the probe file itself. Entry format: "tier_id|base_var|(empty suffix)".
+HOOK_GATE_TIERS=(
+  'gate_adapter_dir|ADAPTER_DIR|'
+  'gate_project|PROJECT_GITHOOKS|'
+  'gate_script_dir|SCRIPT_DIR|'
+)

package/hooks/pre-commit

@@ -15,6 +15,89 @@ SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 ADAPTER_DIR=""
 GLOBAL_ADAPTER_DIR="$HOME/.config/xp-gate/adapters"
 
+# #505: load the resolution-order data BEFORE any tier decision runs. The file is
+# generated from src/npm-package/lib/hook-module-resolution.js, which doctor.js
+# also reads, so the hook and the diagnostic share one order instead of two
+# hand-written copies that a parity test had to keep honest.
+#
+# It is looked up beside the hook (SCRIPT_DIR — always present, since this file
+# IS the hook) and beside adapter-common.sh (ADAPTER_DIR — where `xp-gate init`
+# and setup-global install the supporting modules). Either location works; the
+# hook-dir copy is what `doctor --sync-hooks` and sync-package-content maintain.
+# Note this runs BEFORE ADAPTER_DIR is resolved, which is why the script dir is
+# the primary location: reading the order cannot depend on the order.
+HOOK_RESOLUTION_SH="${SCRIPT_DIR}/hook-module-resolution.sh"
+if [ ! -f "$HOOK_RESOLUTION_SH" ] && [ -f "$GLOBAL_ADAPTER_DIR/hook-module-resolution.sh" ]; then
+  HOOK_RESOLUTION_SH="$GLOBAL_ADAPTER_DIR/hook-module-resolution.sh"
+fi
+if [ ! -f "$HOOK_RESOLUTION_SH" ]; then
+  # Fail closed: a hook that cannot load its resolution order must not fall back
+  # to an invented one — that would silently resurrect the duplication removed
+  # here, and doctor would report a different surface than the hook executes.
+  echo "FATAL: cannot load hook-module-resolution.sh (module resolution order is unavailable)" >&2
+  echo "Fix: reinstall the hooks (xp-gate init, or xp-gate doctor --sync-hooks in the xp-gate repo)." >&2
+  exit 1
+fi
+# shellcheck source=/dev/null
+. "$HOOK_RESOLUTION_SH"
+
+# Look up one tier's directory variable by name without eval-ing arbitrary input:
+# the base names are a closed set baked into the generated file.
+_hook_tier_base() {
+  case "$1" in
+    ADAPTER_DIR)      printf '%s' "$ADAPTER_DIR" ;;
+    GLOBAL_ADAPTER_DIR) printf '%s' "$GLOBAL_ADAPTER_DIR" ;;
+    PROJECT_GITHOOKS) printf '%s' "$PROJECT_GITHOOKS" ;;
+    SCRIPT_DIR)       printf '%s' "$SCRIPT_DIR" ;;
+    *)                printf '%s' "" ;;
+  esac
+}
+
+# Walk a "tier_id|base|suffix" table in order and print the first existing match.
+# Usage: _hook_resolve <module_filename> <tiers_array_name>
+_hook_resolve() {
+  local module_name="$1"
+  local tiers_var="$2"
+  local entry base suffix base_dir candidate
+  eval "set -- \"\${${tiers_var}[@]}\""
+  for entry in "$@"; do
+    entry="${entry#*|}"
+    base="${entry%%|*}"
+    suffix="${entry#*|}"
+    base_dir="$(_hook_tier_base "$base")"
+    [ -n "$base_dir" ] || continue
+    candidate="$base_dir/${suffix/\{name\}/$module_name}"
+    if [ -f "$candidate" ]; then
+      printf '%s' "$candidate"
+      return 0
+    fi
+  done
+  return 1
+}
+
+# Walk a gate tier table and print the first DIRECTORY that contains the probe.
+# The adapter table yields a file; this one yields the directory the gate suite
+# lives in (GATE_DIR), which is why it probes rather than substitutes.
+# Usage: _hook_resolve_dir <probe_filename> <tiers_array_name>
+_hook_resolve_dir() {
+  local probe="$1"
+  local tiers_var="$2"
+  local entry base suffix base_dir
+  eval "set -- \"\${${tiers_var}[@]}\""
+  for entry in "$@"; do
+    entry="${entry#*|}"
+    base="${entry%%|*}"
+    suffix="${entry#*|}"
+    base_dir="$(_hook_tier_base "$base")"
+    [ -n "$base_dir" ] || continue
+    if [ -f "$base_dir${suffix}/$probe" ]; then
+      printf '%s' "$base_dir${suffix}"
+      return 0
+    fi
+  done
+  return 1
+}
+
 # BEGIN GIT CONTEXT FALLBACK
 if ! declare -F run_without_git_context >/dev/null 2>&1; then
   run_without_git_context() (
@@ -51,39 +134,25 @@ source "$ADAPTER_DIR/adapter-common.sh" 2>/dev/null || {
 # ADAPTER_DIR points to the base directory that contains either
 # adapter-common.sh directly (global) or adapter-common.sh in a flat layout.
 # Gate scripts live alongside adapter-common.sh.
+#
+# #505: the ORDER is not written here. HOOK_ADAPTER_TIERS is generated from
+# src/npm-package/lib/hook-module-resolution.js, which doctor.js reads directly,
+# so the hook and the diagnostic cannot disagree about which file wins.
 resolve_adapter_path() {
-  local lang="$1"
-  # Try flat layout first (global: typescript.sh next to adapter-common.sh)
-  if [ -f "$ADAPTER_DIR/${lang}.sh" ]; then
-    echo "$ADAPTER_DIR/${lang}.sh"
-    return 0
-  fi
-  # Try nested layout (project: adapters/typescript.sh)
-  if [ -f "$ADAPTER_DIR/adapters/${lang}.sh" ]; then
-    echo "$ADAPTER_DIR/adapters/${lang}.sh"
-    return 0
-  fi
-  # Try project githooks as fallback
-  if [ -f "$PROJECT_GITHOOKS/adapters/${lang}.sh" ]; then
-    echo "$PROJECT_GITHOOKS/adapters/${lang}.sh"
-    return 0
-  fi
-  # Try script dir as last resort
-  if [ -f "$SCRIPT_DIR/adapters/${lang}.sh" ]; then
-    echo "$SCRIPT_DIR/adapters/${lang}.sh"
-    return 0
-  fi
-  return 1
+  # ADAPTER templates carry the extension ("{name}.sh"), so pass the bare language
+  # name here. GATE templates are "{name}", so their call passes the full filename.
+  _hook_resolve "${1}" HOOK_ADAPTER_TIERS
 }
 
-# Gate scripts directory — falls back to project githooks if ADAPTER_DIR doesn't have them
-if [ -f "$ADAPTER_DIR/gate-3.sh" ]; then
-  GATE_DIR="$ADAPTER_DIR"
-elif [ -f "$PROJECT_GITHOOKS/gate-3.sh" ]; then
-  GATE_DIR="$PROJECT_GITHOOKS"
-elif [ -f "$SCRIPT_DIR/gate-3.sh" ]; then
-  GATE_DIR="$SCRIPT_DIR"
-else
+# Gate scripts directory — falls back to project githooks if ADAPTER_DIR doesn't have them.
+# #505: the probe file and the tier order come from the generated data file, so
+# this cascade cannot drift from what doctor.js reports.
+GATE_DIR="$(_hook_resolve_dir "$HOOK_GATE_PROBE" HOOK_GATE_TIERS)" || GATE_DIR=""
+# Deliberate last resort: when no tier carries the gate suite, point at
+# ADAPTER_DIR anyway rather than leaving GATE_DIR empty. The gate-N.sh sources
+# further down check for the file before sourcing, so an absent suite still
+# degrades to a reported skip instead of a path built from an empty string.
+if [ -z "$GATE_DIR" ]; then
   GATE_DIR="$ADAPTER_DIR"
 fi
 
@@ -3296,7 +3365,14 @@ else
     echo "     ⏭️  SKIPPED - Boy Scout Rule (not available in project)"
   fi
 fi
-GATE_6_STATUS="PASS"
+# A PASS here must mean 'the checks ran and found nothing'. The two
+# branches above print 'SKIPPED - not configured/available'; stamping PASS
+# after them turned 'nothing was checked' into a scored success.
+if [ -n "${GATE_6_STATUS:-}" ]; then
+  : # a branch that really ran already decided the verdict
+else
+  GATE_6_STATUS="SKIP"
+fi
 record_gate_audit "gate-6" "architecture-boy-scout" "$GATE_6_STATUS" "${BS_BLOCKED:-0}" "$GATE_6_START"
 
 # ============================================================================
@@ -3653,7 +3729,10 @@ generate_quality_report() {
     # applicable" and must render and score identically. A previous scoring
     # default of FAIL produced self-contradictory reports -- the gate showed
     # PASS in JSON but scored as FAIL (#507 Delphi round-1 A-MAJOR-2).
-    if [ "$gate" -eq 12 ]; then gate_default="WARN"; else gate_default="PASS"; fi
+    # Default direction is "did not run", never "passed": an unassigned status
+    # is a gate that never reached a verdict, and scoring it PASS both claims a
+    # success that did not happen and hides the gap in the effective rate.
+    if [ "$gate" -eq 12 ]; then gate_default="WARN"; else gate_default="SKIP"; fi
     gate_status="${!status_var:-$gate_default}"
     case "$gate_status" in
       PASS) PASSED_COUNT=$((PASSED_COUNT + 1)) ;;
@@ -3750,7 +3829,7 @@ generate_quality_report() {
     # Gate 6 reason for this language — extracted so the rule is testable
     # rather than inlined (see coverage_g6_reason_for below).
     _cm_g6_reason=$(coverage_g6_reason_for "$_cm_lang")
-    _cm_g6=$(classify_coverage_reason "$_cm_g6_reason" "${GATE_6_STATUS:-PASS}")
+    _cm_g6=$(classify_coverage_reason "$_cm_g6_reason" "${GATE_6_STATUS:-SKIP}")
     _cm_entry="\"${_cm_lang}\": {\"gate3_complexity\": \"${_cm_g3}\", \"gate4_principles\": \"${_cm_g4}\", \"gate6_architecture\": \"${_cm_g6}\"}"
     COVERAGE_MATRIX_JSON="${COVERAGE_MATRIX_JSON:+$COVERAGE_MATRIX_JSON, }${_cm_entry}"
   done
@@ -3786,7 +3865,7 @@ generate_quality_report() {
     },
     "gate2_dup_code": {
       "name": "Duplicate Code",
-      "status": "${GATE_2_STATUS:-PASS}",
+      "status": "${GATE_2_STATUS:-SKIP}",
       "metric": "similarity <= 5%"
     },
     "gate3_complexity": {
@@ -3812,7 +3891,7 @@ generate_quality_report() {
     },
     "gate6_arch_boyscout": {
       "name": "Architecture + Boy Scout Rule",
-      "status": "${GATE_6_STATUS:-PASS}",
+      "status": "${GATE_6_STATUS:-SKIP}",
       "reason": "${GATE_6_REASON:-}",
       "boyScoutPassed": $BS_PASSED,
       "boyScoutBlocked": $BS_BLOCKED
@@ -3865,11 +3944,11 @@ ENDJSON
   # ── History append (unchanged — append-only for trend) ────────────────────────────
   local GATES_JSON="{"
   GATES_JSON="${GATES_JSON}\"gate1\":{\"status\":\"${GATE_1_STATUS:-PASS}\",\"name\":\"Code Quality\"},"
-  GATES_JSON="${GATES_JSON}\"gate2\":{\"status\":\"${GATE_2_STATUS:-PASS}\",\"name\":\"Duplicate Code\"},"
+  GATES_JSON="${GATES_JSON}\"gate2\":{\"status\":\"${GATE_2_STATUS:-SKIP}\",\"name\":\"Duplicate Code\"},"
   GATES_JSON="${GATES_JSON}\"gate3\":{\"status\":\"${GATE_3_STATUS:-PASS}\",\"name\":\"Complexity\",\"warnings\":${CC_WARNINGS:-0}},"
   GATES_JSON="${GATES_JSON}\"gate4\":{\"status\":\"${GATE_4_STATUS:-PASS}\",\"name\":\"Principles\",\"warnings\":${WARNING_COUNT:-0}},"
   GATES_JSON="${GATES_JSON}\"gate5\":{\"status\":\"${GATE_5_STATUS:-PASS}\",\"name\":\"Tests+Coverage\",\"coverage\":\"${COV_PCT}\"},"
-  GATES_JSON="${GATES_JSON}\"gate6\":{\"status\":\"${GATE_6_STATUS:-PASS}\",\"name\":\"Architecture+BoyScout\",\"bsBlocked\":${BS_BLOCKED}},"
+  GATES_JSON="${GATES_JSON}\"gate6\":{\"status\":\"${GATE_6_STATUS:-SKIP}\",\"name\":\"Architecture+BoyScout\",\"bsBlocked\":${BS_BLOCKED}},"
   GATES_JSON="${GATES_JSON}\"gate7\":{\"status\":\"${GATE_7_STATUS:-PASS}\",\"name\":\"IaC Security\"},"
   GATES_JSON="${GATES_JSON}\"gate8\":{\"status\":\"${GATE_8_STATUS:-PASS}\",\"name\":\"Secret Scanning\"},"
   GATES_JSON="${GATES_JSON}\"gate9\":{\"status\":\"${GATE_9_STATUS:-PASS}\",\"name\":\"Build Integrity\"},"
@@ -3886,11 +3965,11 @@ ENDJSON
   echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
   echo ""
   printf "  %-45s %s\n" "Gate 1: Code Quality" "${GATE_1_STATUS:-PASS}"
-  printf "  %-45s %s\n" "Gate 2: Duplicate Code" "${GATE_2_STATUS:-PASS}"
+  printf "  %-45s %s\n" "Gate 2: Duplicate Code" "${GATE_2_STATUS:-SKIP}"
   printf "  %-45s %s (warnings: ${CC_WARNINGS:-0})\n" "Gate 3: Complexity" "${GATE_3_STATUS:-PASS}"
   printf "  %-45s %s (warnings: ${WARNING_COUNT:-0})\n" "Gate 4: Principles" "${GATE_4_STATUS:-PASS}"
   printf "  %-45s %s (coverage: ${COV_PCT}%%)\n" "Gate 5: Tests + Coverage" "${GATE_5_STATUS:-PASS}"
-  printf "  %-45s %s\n" "Gate 6: Architecture + Boy Scout" "${GATE_6_STATUS:-PASS}"
+  printf "  %-45s %s\n" "Gate 6: Architecture + Boy Scout" "${GATE_6_STATUS:-SKIP}"
   printf "  %-45s %s\n" "Gate 7: IaC Security" "${GATE_7_STATUS:-PASS}"
   printf "  %-45s %s\n" "Gate 8: Secret Scanning" "${GATE_8_STATUS:-PASS}"
   printf "  %-45s %s\n" "Gate 9: Build Integrity" "${GATE_9_STATUS:-PASS}"

package/hooks/pre-push

@@ -51,7 +51,7 @@ report = {
   'gates': [
     {'id': 'MP', 'name': 'Gate-Script Mirror Parity', 'status': '${GATE_MP_STATUS:-SKIP}', 'details': {'duration_ms': '${MP_DURATION_MS:-0}'}},
     {'id': '10', 'name': 'Build Integrity', 'status': '${GATE_10_STATUS:-SKIP}', 'details': {}},
-    {'id': 'M', 'name': 'Mutation Testing', 'status': '${GATE_M_STATUS:-SKIP}', 'details': {}},
+    {'id': 'M', 'name': 'Mutation Testing', 'status': '${GATE_M_STATUS:-SKIP}', 'details': {'skip_reason': '${GATE_M_SKIP_REASON:-}', 'duration_ms': '${M_DURATION_MS:-0}', 'mutation_score': '${M_SCORE:-}'}},
     {'id': 'M-Python', 'name': 'Mutation Testing (Python)', 'status': '${GATE_M_PYTHON_STATUS:-SKIP}', 'details': {}},
     {'id': 'M-Go', 'name': 'Mutation Testing (Go)', 'status': '${GATE_M_GO_STATUS:-SKIP}', 'details': {}},
     {'id': 'M-Java', 'name': 'Mutation Testing (Java)', 'status': '${GATE_M_JAVA_STATUS:-SKIP}', 'details': {}},
@@ -373,16 +373,22 @@ fi
 # shellcheck source=githooks/adapter-common.sh
 source "$ADAPTER_COMMON" 2>/dev/null || {
   echo "⚠️ Could not source adapter-common.sh. SKIP — Gate M."
+  GATE_M_SKIP_REASON="adapter-common.sh could not be sourced"
 }
 
-# Only run for TypeScript projects
+# #404 P0: every Gate M skip records WHY. Without this the journals carried
+# `details: {}` on 62 of 68 runs, so the RFC's "SKIP rate" question was
+# unanswerable — a missing tool and "no mutable file in this push" are opposite
+# findings that looked identical after the fact.
 if [[ ! -f "package.json" ]] || [[ ! -f "tsconfig.json" ]]; then
   echo "📚 Not a TypeScript project. SKIP — Gate M."
+  GATE_M_SKIP_REASON="not a TypeScript project (package.json+tsconfig.json required)"
 else
   # Check if mutation testing is configured
   if ! detect_mutation_testable 2>/dev/null; then
     echo "⚠️ Stryker config not found or @stryker-mutator not installed."
     echo "   SKIP — Gate M mutation testing."
+    GATE_M_SKIP_REASON="stryker config missing or @stryker-mutator not installed"
   else
     # Filter to source files (exclude tests). The tree-segment grep excludes
     # test infrastructure (helpers/fixtures under tests/, test/, __tests__/)
@@ -392,6 +398,7 @@ else
 
     if [ -z "$CHANGED_SOURCE_FILES" ]; then
       echo "📚 No changed TypeScript source files. SKIP — Gate M."
+      GATE_M_SKIP_REASON="no changed TypeScript source files in this push"
     else
       echo "🧬 Running mutation tests on changed files..."
       echo "$CHANGED_SOURCE_FILES"
@@ -408,15 +415,28 @@ else
 
       if [[ -z "$MUTATION_SCRIPT" ]]; then
         echo "⚠️ Gate M script not found. SKIP — Gate M."
+        GATE_M_SKIP_REASON="gate-m.ts not found in .xp-gate/modules, src/mutation, or global modules"
       else
         # Run mutation gate with timeout matching stryker.conf.json (timeoutMS: 600000 = 10min)
         MUTATION_OUTPUT=$(mktemp)
+        M_START_MS=$(date +%s%3N 2>/dev/null || python -c 'import time;print(int(time.time()*1000))' 2>/dev/null || echo 0)
         RUN_TSX_TIMEOUT=600s run_tsx $MUTATION_SCRIPT --changed-files "$CHANGED_SOURCE_FILES" > "$MUTATION_OUTPUT" 2>&1
         MUTATION_EXIT=$?
+        M_END_MS=$(date +%s%3N 2>/dev/null || python -c 'import time;print(int(time.time()*1000))' 2>/dev/null || echo 0)
+        if [ "$M_START_MS" != "0" ] && [ "$M_END_MS" != "0" ]; then
+          M_DURATION_MS=$((M_END_MS - M_START_MS))
+          [ "$M_DURATION_MS" -ge 0 ] || M_DURATION_MS=0
+        else
+          M_DURATION_MS=0
+        fi
+        # #404: the mutation score is the number the RFC wants a distribution for.
+        # It is printed by gate-m.ts; take the last percentage it reported.
+        M_SCORE=$(sed -n 's/.*[Mm]utation score[: ]*\([0-9][0-9]*\(\.[0-9][0-9]*\)\?\)%.*/\1/p' "$MUTATION_OUTPUT" 2>/dev/null | tail -1)
 
         case $MUTATION_EXIT in
           0)
             echo "✅ Gate M: PASS"
+            GATE_M_STATUS="PASS"
             # Update baseline after successful mutation test
             if [ -f ".stryker-baseline.json" ]; then
               echo "📝 Updating mutation baseline..."
@@ -437,11 +457,15 @@ else
           124)
             echo "⏱️ Gate M: TIMEOUT (120s). Mutation testing incomplete."
             echo "   Allowing push with warning — review mutation coverage manually."
+            GATE_M_STATUS="TIMEOUT"
+            GATE_M_SKIP_REASON="mutation run exceeded the 600s timeout; score is unknown"
             ;;
           *)
             echo "⚠️ Gate M: Unexpected exit code $MUTATION_EXIT"
             cat "$MUTATION_OUTPUT"
             echo "   Allowing push with warning."
+            GATE_M_STATUS="WARN"
+            GATE_M_SKIP_REASON="gate-m.ts exited $MUTATION_EXIT (unexpected); score is unknown"
             ;;
         esac
 

package/lib/__tests__/doctor-module-resolution-parity.test.js

@@ -16,10 +16,20 @@
 import { mkdtempSync, mkdirSync, writeFileSync, readFileSync, existsSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join, resolve } from 'node:path';
-import { spawnSync } from 'node:child_process';
+import { spawnSync, execFileSync } from 'node:child_process';
 import { describe, expect, it } from 'vitest';
 
 const PRE_COMMIT = readFileSync(resolve(__dirname, '..', '..', '..', '..', 'githooks', 'pre-commit'), 'utf8');
+// #505 replaced the two hand-written shell chains with one data file generated
+// from lib/hook-module-resolution.js — the same module doctor.js requires. The
+// parity test therefore verifies the NEW contract: the generated data is current,
+// and the hook + doctor both honour it. The scenarios below still drive the hook's
+// real text through bash, so agreement is measured, not asserted.
+const RESOLUTION_DATA = readFileSync(
+  resolve(__dirname, '..', '..', '..', '..', 'githooks', 'hook-module-resolution.sh'),
+  'utf8',
+);
+const { RESOLUTION_ORDER, GATE_RESOLUTION_ORDER, ADAPTER_DIR_ORDER } = require('../hook-module-resolution.js');
 
 /**
  * Extract one bash function's full text, brace-balanced from the declaration.
@@ -149,13 +159,28 @@ function hookResolvesAll(blocks, resolverText, t, lang, gateModule) {
     `GLOBAL_ADAPTER_DIR='${t.globalAdapters}'`,
     `PROJECT_GITHOOKS='${t.projectGithooks}'`,
     `SCRIPT_DIR='${t.scriptDir}'`,
-    blocks.adapterDir,
+    `ADAPTER_DIR=''`,
+    resolverText,
     blocks.gateDir,
+    // The real chains, driven by the same data the hook loads.
+    '_hook_adapter_dir() {',
+    '  local entry base suffix base_dir',
+    '  eval "set -- \\"\\${HOOK_ADAPTER_DIR_TIERS[@]}\\""',
+    '  for entry in "$@"; do',
+    '    entry="${entry#*|}"; base="${entry%%|*}"; suffix="${entry#*|}"',
+    '    base_dir="$(_hook_tier_base "$base")"',
+    '    [ -n "$base_dir" ] || continue',
+    '    if [ -f "$base_dir/$suffix" ]; then printf "%s" "$base_dir"; return 0; fi',
+    '  done',
+    '  return 1',
+    '}',
+    'ADAPTER_DIR="$(_hook_adapter_dir)" || ADAPTER_DIR="$SCRIPT_DIR"',
+    'GATE_DIR="$(_hook_resolve_dir "$HOOK_GATE_PROBE" HOOK_GATE_TIERS)" || GATE_DIR=""',
+    'if [ -z "$GATE_DIR" ]; then GATE_DIR="$ADAPTER_DIR"; fi',
     'echo "ADAPTER=$ADAPTER_DIR"',
     'echo "GATE=$GATE_DIR"',
     `if [ -f "$ADAPTER_DIR/adapter-common.sh" ]; then echo "COMMON=$ADAPTER_DIR/adapter-common.sh"; else echo "COMMON="; fi`,
     `if [ -f "$GATE_DIR/${gateModule}" ]; then echo "MODULE=$GATE_DIR/${gateModule}"; else echo "MODULE="; fi`,
-    resolverText,
     // Captured by substitution rather than read off the last stdout line: the
     // script ends with a newline, so "last line" is always the empty one.
     `echo "LANG=$(resolve_adapter_path ${lang} || true)"`,
@@ -194,14 +219,53 @@ function hookResolves(fnText, tree, lang) {
 }
 
 describe('doctor module resolution parity with pre-commit (#495)', () => {
-  const resolverText = extractFunction(PRE_COMMIT, 'resolve_adapter_path() {');
-  // The two tier chains the hook runs before it ever calls the resolver. Read
-  // from the hook's text, not restated here: #495 Round 2's project-tier label
-  // was wrong precisely because doctor carried a second, hand-written tier list.
+  // #505: the resolver helpers come from the hook, the tier DATA from the
+  // generated file. Concatenating them is what the hook itself does, so the
+  // bash side here is the production code path, not a paraphrase of it.
+  const helpers = [
+    extractFunction(PRE_COMMIT, '_hook_tier_base() {'),
+    extractFunction(PRE_COMMIT, '_hook_resolve() {'),
+    extractFunction(PRE_COMMIT, '_hook_resolve_dir() {'),
+    extractFunction(PRE_COMMIT, 'resolve_adapter_path() {'),
+  ].join('\n');
+  // `blocks` keeps the names the scenarios use: the data file supplies the
+  // ADAPTER_DIR/GATE_DIR chains that used to be matched out of the hook text.
   const blocks = {
-    adapterDir: matchBlock(PRE_COMMIT, /if \[ -f "\$GLOBAL_ADAPTER_DIR\/adapter-common\.sh" \]; then[\s\S]*?\nfi/, 'the ADAPTER_DIR tier chain'),
-    gateDir: matchBlock(PRE_COMMIT, /if \[ -f "\$ADAPTER_DIR\/gate-3\.sh" \]; then[\s\S]*?\nfi/, 'the GATE_DIR tier chain'),
+    adapterDir: '',
+    gateDir: '',
   };
+  const resolverText = `${RESOLUTION_DATA}\n${helpers}`;
+
+  it('AC-505-01: the generated shell data is current with its JS source', () => {
+    // Stale data would silently run a different order than doctor reports — the
+    // exact failure mode #505 exists to make impossible.
+    expect(() => execFileSync(
+      process.execPath,
+      [resolve(__dirname, '..', '..', '..', '..', 'scripts', 'generate-hook-resolution.cjs'), '--check'],
+      { stdio: 'pipe' },
+    )).not.toThrow();
+  });
+
+  it('AC-505-02: the hook loads the generated data instead of carrying its own order', () => {
+    // Anti-vacuity for the whole feature: if the hook re-grew a literal cascade,
+    // the single-source-of-truth claim would be false even while scenarios pass.
+    expect(PRE_COMMIT).toContain('hook-module-resolution.sh');
+    expect(PRE_COMMIT).toContain('HOOK_ADAPTER_TIERS');
+    expect(PRE_COMMIT).toContain('HOOK_GATE_TIERS');
+    // The old hand-written chains must be gone.
+    expect(PRE_COMMIT).not.toContain('$ADAPTER_DIR/${lang}.sh');
+    expect(PRE_COMMIT).not.toMatch(/if \[ -f "\$ADAPTER_DIR\/gate-3\.sh" \]; then/);
+    // And every tier the JS declares must appear in the emitted shell data.
+    for (const t of RESOLUTION_ORDER) {
+      expect(RESOLUTION_DATA).toContain(`${t.tier_id}|${t.base}|${t.template}`);
+    }
+    for (const t of GATE_RESOLUTION_ORDER) {
+      expect(RESOLUTION_DATA).toContain(`'${t.tier_id}|${t.base}|'`);
+    }
+    for (const t of ADAPTER_DIR_ORDER) {
+      expect(RESOLUTION_DATA).toContain(`${t.tier_id}|${t.base}|${t.probe}`);
+    }
+  });
 
   it('AC-495-11: flat and nested present -> both languages pick the flat copy', () => {
     const { listExecutedModules } = require('../doctor');
@@ -241,8 +305,12 @@ describe('doctor module resolution parity with pre-commit (#495)', () => {
     }
 
     // Anti-vacuity: the guard executed the hook's real text, not a paraphrase.
-    expect(resolverText).toMatch(/\$ADAPTER_DIR\/\$\{lang\}\.sh/);
-    expect(resolverText).toMatch(/\$ADAPTER_DIR\/adapters\/\$\{lang\}\.sh/);
+    // #505 moved the literal paths out of the hook, so assert that the tiers it
+    // now reads still describe the two layouts those paths used to spell out.
+    expect(resolverText).toContain('HOOK_ADAPTER_TIERS');
+    const adapterTemplates = RESOLUTION_ORDER.map((t) => t.template);
+    expect(adapterTemplates).toContain('{name}.sh');
+    expect(adapterTemplates).toContain('adapters/{name}.sh');
   });
 
   // The scenarios below put a copy of the same module in EVERY tier the hook can

package/lib/__tests__/sprint-state-manager.test.js

@@ -143,6 +143,37 @@ describe('SprintStateManager', () => {
       expect(result.phase_history[0].duration_seconds).toBeGreaterThanOrEqual(0);
     });
 
+    it('stamps a duration when a phase goes straight from pending to completed', () => {
+      // Regression: `xp-gate phase-transition N completed --render` never emits
+      // an in_progress step, so gating started_at on in_progress left
+      // duration_seconds permanently null — the blank duration column on the
+      // status panel. Observed on sprint-20261019-47 phases 2-6.
+      const initialState = createInitialState(tmpDir);
+      manager.write(initialState);
+
+      const result = manager.transitionPhase(2, 'completed');
+
+      expect(result.phase_history[0].status).toBe('completed');
+      expect(result.phase_history[0].started_at).toBeDefined();
+      expect(result.phase_history[0].completed_at).toBeDefined();
+      expect(result.phase_history[0].duration_seconds).not.toBeNull();
+      expect(result.phase_history[0].duration_seconds).toBeGreaterThanOrEqual(0);
+      expect(Number.isNaN(result.phase_history[0].duration_seconds)).toBe(false);
+    });
+
+    it('never writes a NaN duration, even for an unparseable started_at', () => {
+      const state = createInitialState(tmpDir);
+      state.phase_history = [
+        { phase: 2, phase_name: 'DESIGN', status: 'pending', started_at: 'not-a-date' },
+      ];
+      manager.write(state);
+
+      const result = manager.transitionPhase(2, 'completed');
+
+      expect(Number.isNaN(result.phase_history[0].duration_seconds)).toBe(false);
+      expect(result.phase_history[0].duration_seconds).toBe(0);
+    });
+
     it('calls onTransition callback', () => {
       const initialState = createInitialState(tmpDir);
       manager.write(initialState);