phasegate 0.160.5 → 0.160.7

package/CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.160.6] - 2026-05-14
+
+### Fixed
+
+- **WI-190..WI-196 — post-0.160.5 dogfood regressions** — aligns agent context refresh with reconcile rendering, adds retrofit planning-mode config plans, makes cascade update dry-runs non-mutating and explicit, fixes doctor `_shared` drift counts, removes pnpm-only scheduled CI templates, exposes `migrate work-items` help, and accepts positional `delegate-sonnet` prompts.
+
 ## [0.160.5] - 2026-05-14
 
 ### Fixed

package/docs/templates/ci/agent-context-refresh.yml

@@ -1,4 +1,5 @@
 # Phasegate — Agent context refresh workflow
+# @work-item-id WI-194
 #
 # 使い方:
 #   このファイルを .github/workflows/agent-context-refresh.yml にコピーして使用する。
@@ -32,18 +33,21 @@ jobs:
         uses: actions/setup-node@v4
         with:
           node-version: '20'
-          cache: 'pnpm'
-
-      - name: Install pnpm
-        uses: pnpm/action-setup@v4
-        with:
-          version: 9
 
       - name: Install dependencies
-        run: pnpm install --frozen-lockfile
+        run: |
+          if [ -f pnpm-lock.yaml ]; then
+            pnpm install --frozen-lockfile
+          elif [ -f yarn.lock ]; then
+            yarn install --immutable || yarn install --frozen-lockfile
+          elif [ -f package-lock.json ] || [ -f npm-shrinkwrap.json ]; then
+            npm ci
+          else
+            npm install
+          fi
 
       - name: Refresh agent context
-        run: pnpm run harness ci:auto-refresh-agent-context --apply
+        run: npx phasegate ci:auto-refresh-agent-context --apply
 
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6

package/docs/templates/ci/consistency-check.yml

@@ -1,4 +1,5 @@
 # Phasegate — 週次整合性チェックワークフロー
+# @work-item-id WI-194
 #
 # 使い方:
 #   このファイルを .github/workflows/consistency-check.yml にコピーして使用する。
@@ -31,15 +32,18 @@ jobs:
         uses: actions/setup-node@v4
         with:
           node-version: '20'
-          cache: 'pnpm'
-
-      - name: Install pnpm
-        uses: pnpm/action-setup@v4
-        with:
-          version: 9
 
       - name: Install dependencies
-        run: pnpm install --frozen-lockfile
+        run: |
+          if [ -f pnpm-lock.yaml ]; then
+            pnpm install --frozen-lockfile
+          elif [ -f yarn.lock ]; then
+            yarn install --immutable || yarn install --frozen-lockfile
+          elif [ -f package-lock.json ] || [ -f npm-shrinkwrap.json ]; then
+            npm ci
+          else
+            npm install
+          fi
 
       # L4-001: Drift Detection（設計⇔コード双方向乖離）
       - name: L4 Drift Detection

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "phasegate",
-  "version": "0.160.5",
+  "version": "0.160.7",
   "packageManager": "pnpm@10.30.1",
   "description": "Phasegate — AI-agnostic quality defense toolkit. Enforces structural integrity between design intent and code.",
   "license": "MIT",

package/scripts/delegate-sonnet.sh

@@ -4,11 +4,12 @@
 # Usage:
 #   bash scripts/delegate-sonnet.sh --prompt "プロンプト" --output "出力パス"
 #   bash scripts/delegate-sonnet.sh --prompt-file /tmp/prompt.md --output "出力パス"
+#   bash scripts/delegate-sonnet.sh "プロンプト" --output "出力パス"
 #
 # Options:
 #   --prompt        委任プロンプト（直接指定、2000文字以下推奨）
 #   --prompt-file   委任プロンプトファイル（長文の場合）
-#   --output        出力ファイルパス
+#   --output        出力ファイルパス（省略時: .phasegate/delegate-sonnet-output.md）
 #   --max-turns     最大ターン数（デフォルト: 30）
 #   --dry-run       プロンプトを表示するだけで実行しない
 
@@ -20,6 +21,7 @@ PROMPT_FILE=""
 OUTPUT_PATH=""
 MAX_TURNS=30
 DRY_RUN=false
+POSITIONAL_ARGS=()
 
 while [[ $# -gt 0 ]]; do
   case $1 in
@@ -43,23 +45,35 @@ while [[ $# -gt 0 ]]; do
       DRY_RUN=true
       shift
       ;;
+    --)
+      shift
+      if [[ $# -gt 0 ]]; then
+        POSITIONAL_ARGS+=("$@")
+      fi
+      break
+      ;;
     *)
-      echo "Unknown option: $1" >&2
-      exit 1
+      if [[ "$1" == --* ]]; then
+        echo "Unknown option: $1" >&2
+        exit 1
+      fi
+      POSITIONAL_ARGS+=("$1")
+      shift
       ;;
   esac
 done
 
+if [[ -z "$PROMPT" && ${#POSITIONAL_ARGS[@]} -gt 0 ]]; then
+  PROMPT="${POSITIONAL_ARGS[*]}"
+fi
+
 # --- バリデーション ---
 if [[ -z "$PROMPT" && -z "$PROMPT_FILE" ]]; then
   echo "Error: --prompt or --prompt-file is required" >&2
   exit 1
 fi
 
-if [[ -z "$OUTPUT_PATH" ]]; then
-  echo "Error: --output is required" >&2
-  exit 1
-fi
+OUTPUT_PATH="${OUTPUT_PATH:-.phasegate/delegate-sonnet-output.md}"
 
 if [[ -n "$PROMPT_FILE" && ! -f "$PROMPT_FILE" ]]; then
   echo "Error: Prompt file not found: $PROMPT_FILE" >&2

package/scripts/harness/ci-governance/application/usecases/refresh-claude-md-usecase.ts

@@ -1,6 +1,7 @@
 /**
  * @layer application
  * @unit ci-governance
+ * @work-item-id WI-190
  */
 
 import type { AgentContextDocumentPort } from '../../domain/ports/agent-context-document-port.js';
@@ -12,12 +13,11 @@ const CLAUDE_MD_PATH = 'CLAUDE.md';
 const CLAUDE_MD_TEMPLATE_PATH = 'docs/templates/agent-context/CLAUDE.md.template.md';
 
 const PHASEGATE_COMMANDS = [
-  'phasegate init --with-ci',
-  'phasegate ci:auto-refresh-agent-context --dry-run',
-  'phasegate ci:auto-refresh-agent-context --apply',
-  'phasegate refresh-claude-md --apply',
-  'phasegate p2:check-agent-context',
+  'phasegate doctor',
   'phasegate phasegate:check-ready',
+  'phasegate validate --layer L2 --format human',
+  'phasegate setup:agent --dry-run',
+  'phasegate config:plan --intent l4-strict --dry-run',
 ];
 
 const PHASE_PRESETS = ['minimal', 'standard', 'full', 'custom'];
@@ -37,7 +37,7 @@ export class RefreshClaudeMdUseCase {
       ]);
       const nextContent = this.composer.compose(template, existing, {
         commands: PHASEGATE_COMMANDS,
-        skills,
+        skills: ['all bundled skills'],
         presets: PHASE_PRESETS,
       });
       const changed = existing !== nextContent;

package/scripts/harness/ci-governance/domain/services/claude-md-composer.ts

@@ -11,7 +11,7 @@ export interface ClaudeMdTemplateValues {
 
 const USER_SECTION_START = '<!-- phasegate:user-section:start -->';
 const USER_SECTION_END = '<!-- phasegate:user-section:end -->';
-const DEFAULT_USER_SECTION = 'プロジェクト固有の指示をここに記載してください。';
+const DEFAULT_USER_SECTION = 'Project-specific agent instructions go here.';
 
 export class ClaudeMdComposer {
   compose(template: string, existing: string | null, values: ClaudeMdTemplateValues): string {

package/scripts/harness/ci-governance/infrastructure/adapters/yaml-template-renderer-adapter.ts

@@ -2,6 +2,7 @@
  * @layer infrastructure
  * @unit ci-governance
  * @work-item-id WI-182 / WI-183
+ * @work-item-id WI-194
  *
  * TemplateRendererPort実装（YAML書き出し）
  */

package/scripts/harness/ci-governance/presentation/formatters/ci-template-formatter.ts

@@ -1,6 +1,7 @@
 /**
  * @layer presentation
  * @unit ci-governance
+ * @work-item-id WI-200
  */
 
 import type { GenerateCiTemplateOutput } from '../../application/dto/generate-ci-template-output.js';
@@ -15,12 +16,13 @@ export class CiTemplateFormatter {
         lines.push(`  [${err.code}] ${err.message}`);
       }
     } else {
-      lines.push('✓ CI Template Generated');
+      lines.push('✓ CI Template Plan Ready');
       lines.push(`  Template Type: ${output.templateType}`);
       lines.push(`  Preset: ${output.presetRef}`);
       lines.push(`  Trigger: ${output.triggerCondition}`);
       lines.push(`  Validators: ${output.targetValidatorIds.join(', ')}`);
       lines.push(`  Fail on Warning: ${output.failOnWarning}`);
+      lines.push('  Output: no file written; use --render to print template YAML');
     }
 
     return lines.join('\n');

package/scripts/harness/config-foundation/domain/harness-config.ts

@@ -29,7 +29,7 @@ import type {
 
 export type LayerId = 'L1' | 'L2' | 'L3' | 'L4';
 export type PresetId = 'minimal' | 'standard' | 'strict';
-export type PlanningModeValue = 'interactive' | 'embedded-qa';
+export type PlanningModeValue = 'interactive' | 'embedded-qa' | 'manual';
 export type { PhaseDependenciesPresetId };
 type DeepPartial<T> = {
   [K in keyof T]?: T[K] extends Array<infer TItem>

package/scripts/harness/config-foundation/domain/value-objects/planning-mode-config.ts

@@ -3,11 +3,11 @@
  * @unit config-foundation
  *
  * Planning Mode設定を表す値オブジェクト
- * defaultMode と perPhase の値は列挙値 "interactive" | "embedded-qa" のみ許容
+ * defaultMode と perPhase の値は列挙値 "interactive" | "embedded-qa" | "manual" のみ許容
  */
 import { ConfigValidationError } from '../errors/config-validation-error.js';
 
-const VALID_MODES = ['interactive', 'embedded-qa'] as const;
+const VALID_MODES = ['interactive', 'embedded-qa', 'manual'] as const;
 type PlanningMode = (typeof VALID_MODES)[number];
 
 export interface PlanningModeConfigProps {

package/scripts/harness/config-foundation/infrastructure/schemas/harness-config-v2.schema.json

@@ -384,7 +384,8 @@
           "type": "string",
           "enum": [
             "interactive",
-            "embedded-qa"
+            "embedded-qa",
+            "manual"
           ]
         },
         "perPhase": {
@@ -393,7 +394,8 @@
             "type": "string",
             "enum": [
               "interactive",
-              "embedded-qa"
+              "embedded-qa",
+              "manual"
             ]
           }
         }

package/scripts/harness/config-foundation/infrastructure/schemas/harness-config-v3.schema.json

@@ -394,7 +394,8 @@
           "type": "string",
           "enum": [
             "interactive",
-            "embedded-qa"
+            "embedded-qa",
+            "manual"
           ]
         },
         "perPhase": {
@@ -403,7 +404,8 @@
             "type": "string",
             "enum": [
               "interactive",
-              "embedded-qa"
+              "embedded-qa",
+              "manual"
             ]
           }
         }

package/scripts/harness/installation/application/checks/wi-workflow-drift-check.ts

@@ -2,6 +2,7 @@
 // @layer application
 // @work-item-id WI-143
 // @work-item-id WI-187
+// @work-item-id WI-193
 
 import { join, relative, sep } from "node:path";
 import { DiagnosticFinding } from "../../domain/diagnostic-finding.js";
@@ -61,5 +62,6 @@ function isWorkItemDescription(path: string): boolean {
 function isAdHocPlan(path: string): boolean {
   if (!path.startsWith("docs/inception/")) return false;
   if (/\/WI-\d{3}\//.test(path)) return false;
+  if (path.startsWith("docs/inception/_shared/") && path.endsWith(".md")) return true;
   return path.includes("/codding_plan/") || path.endsWith("_plan.md");
 }

package/scripts/harness/installation/application/usecases/run-install.ts

@@ -2,6 +2,7 @@
 // @layer application
 // @work-item-id WI-146
 // @work-item-id WI-174
+// @work-item-id WI-198
 // @work-item-id WI-175
 // @work-item-id WI-177
 // @work-item-id WI-182
@@ -190,7 +191,7 @@ function renderAgentContextTemplate(
     .replaceAll("{{PHASEGATE_HUSKY_STATE}}", options.includeHusky ? "managed" : "not managed by this setup run")
     .replaceAll("{{PHASEGATE_CI_STATE}}", options.includeCi ? "managed" : "not managed by this setup run")
     .replaceAll("{{PHASEGATE_COMMANDS}}", commands)
-    .replaceAll("{{PHASEGATE_SKILLS}}", options.skillSet === "core" ? "- core skills" : "- all bundled skills")
+    .replaceAll("{{PHASEGATE_SKILLS}}", options.skillSet === "core" ? "- `core skills`" : "- `all bundled skills`")
     .replaceAll("{{PHASEGATE_PRESETS}}", "- `minimal`\n- `standard`\n- `full`\n- `custom`")
     .replaceAll("{{PHASEGATE_USER_SECTION}}", "Project-specific agent instructions go here.");
 }

package/scripts/harness/installation/application/usecases/run-reconcile.ts

@@ -2,6 +2,7 @@
 // @layer application
 // @work-item-id WI-148
 // @work-item-id WI-174
+// @work-item-id WI-198
 
 import { access, chmod, copyFile, lstat, mkdir, readFile, readlink, symlink, writeFile } from "node:fs/promises";
 import { dirname, join, relative, resolve } from "node:path";
@@ -156,12 +157,12 @@ function reconcileManagedMarkdown(existing: string | null, incoming: string): st
 
 function renderAgentContextTemplate(template: string): string {
   const commands = [
-    "- `phasegate doctor`",
-    "- `phasegate phasegate:check-ready`",
-    "- `phasegate validate --layer L2 --format human`",
-    "- `phasegate setup:agent --dry-run`",
-    "- `phasegate config:plan --intent l4-strict --dry-run`",
-  ].join("\n");
+    "phasegate doctor",
+    "phasegate phasegate:check-ready",
+    "phasegate validate --layer L2 --format human",
+    "phasegate setup:agent --dry-run",
+    "phasegate config:plan --intent l4-strict --dry-run",
+  ].map((command) => `- \`${command}\``).join("\n");
   return template
     .replaceAll("{{PHASEGATE_AGENT}}", "both")
     .replaceAll("{{PHASEGATE_SKILLS_MODE}}", "all")
@@ -169,7 +170,7 @@ function renderAgentContextTemplate(template: string): string {
     .replaceAll("{{PHASEGATE_HUSKY_STATE}}", "managed")
     .replaceAll("{{PHASEGATE_CI_STATE}}", "managed")
     .replaceAll("{{PHASEGATE_COMMANDS}}", commands)
-    .replaceAll("{{PHASEGATE_SKILLS}}", "- all bundled skills")
+    .replaceAll("{{PHASEGATE_SKILLS}}", "- `all bundled skills`")
     .replaceAll("{{PHASEGATE_PRESETS}}", "- `minimal`\n- `standard`\n- `full`\n- `custom`")
     .replaceAll("{{PHASEGATE_USER_SECTION}}", "Project-specific agent instructions go here.");
 }
@@ -299,7 +300,7 @@ export class RunReconcileUseCase {
     const matchesManifest = currentHash.equals(entry.hash);
     const rawTemplate = target.templatePath ? await readFile(join(input.harnessRoot, target.templatePath), "utf8") : "";
     const template = target.strategy === "markdown-managed" ? renderAgentContextTemplate(rawTemplate) : rawTemplate;
-    const next = entry.mode === "created" && target.strategy !== "package-json"
+    const next = entry.mode === "created" && target.strategy !== "package-json" && target.strategy !== "markdown-managed"
       ? template
       : this.reconcileContent(target, before, template, input.phasegateVersion);
     const changed = before !== next;

package/scripts/harness/installation/application/usecases/run-uninstall.ts

@@ -2,6 +2,7 @@
 // @layer application
 // @work-item-id WI-147
 // @work-item-id WI-174
+// @work-item-id WI-199
 
 import { access, copyFile, lstat, mkdir, readFile, readlink, rm, rmdir, writeFile } from "node:fs/promises";
 import { dirname, join, relative, resolve } from "node:path";
@@ -19,6 +20,7 @@ export interface UninstallPlanItem {
   readonly repairMode: RepairMode;
   readonly strategy: StrategyType;
   readonly changed: boolean;
+  readonly protected: boolean;
   readonly summary: string;
   readonly diff: string;
   readonly skillHint: string | null;
@@ -46,6 +48,7 @@ const SHELL_END = "# === phasegate managed (END) ===";
 const MARKDOWN_BEGIN = "<!-- phasegate:managed-section:start -->";
 const MARKDOWN_END = "<!-- phasegate:managed-section:end -->";
 const PHASEGATE_SCRIPT_PREFIX = "phasegate:";
+const PROTECTED_UNINSTALL_PATHS = new Set(["package.json", "package-lock.json"]);
 
 function isRecord(value: unknown): value is Record<string, unknown> {
   return typeof value === "object" && value !== null && !Array.isArray(value);
@@ -175,7 +178,7 @@ export class RunUninstallUseCase {
       const outcome = await this.planEntry(input, entry);
       outcomes.push({ entry, ...outcome });
       plan.push(outcome.item);
-      if (input.apply && outcome.item.changed && (outcome.item.repairMode === "ai-assisted" || outcome.item.repairMode === "manual") && !input.force) {
+      if (input.apply && outcome.item.changed && this.requiresForce(outcome.item) && !input.force) {
         refused.push({ ...outcome.item, action: "refuse" });
       }
     }
@@ -372,6 +375,14 @@ export class RunUninstallUseCase {
     diff: string,
     skillHint: string | null,
   ): UninstallPlanItem {
-    return { path, action, repairMode, strategy, changed, summary, diff, skillHint };
+    return { path, action, repairMode, strategy, changed, protected: this.isProtectedPath(path), summary, diff, skillHint };
+  }
+
+  private requiresForce(item: UninstallPlanItem): boolean {
+    return item.protected || item.repairMode === "ai-assisted" || item.repairMode === "manual";
+  }
+
+  private isProtectedPath(path: string): boolean {
+    return PROTECTED_UNINSTALL_PATHS.has(path);
   }
 }

package/scripts/harness/installation/presentation/cli/uninstall-handler.ts

@@ -1,6 +1,7 @@
 // @unit installation
 // @layer presentation
 // @work-item-id WI-147
+// @work-item-id WI-199
 
 import type { RunUninstallUseCase } from "../../application/usecases/run-uninstall.js";
 
@@ -33,14 +34,15 @@ export class UninstallHandler {
       input.apply ? "phasegate uninstall apply" : "phasegate uninstall dry-run",
       ...result.plan.map((item) => {
         const hint = item.skillHint ? `; hint: ${item.skillHint}` : "";
-        return `- ${item.path}: ${item.action} (${item.repairMode}, ${item.strategy}); diff: ${item.diff}${hint}`;
+        const protectedMarker = item.protected ? "; protected: true" : "";
+        return `- ${item.path}: ${item.action} (${item.repairMode}, ${item.strategy}${protectedMarker}); diff: ${item.diff}${hint}`;
       }),
     ];
     if (result.backupDir !== null) lines.push(`backups: ${result.backupDir}`);
     if (result.archivedManifestPath !== null) lines.push(`archived manifest: ${result.archivedManifestPath}`);
     if (result.refused.length > 0) {
       lines.push("");
-      lines.push("Refused ai-assisted/manual targets. Re-run with --force after reviewing the hint.");
+      lines.push("Refused protected, ai-assisted, or manual targets. Re-run with --force after reviewing the plan.");
     }
     return {
       stdout: lines.join("\n"),

package/scripts/harness/main.ts

@@ -8,6 +8,11 @@
  * @work-item-id WI-176
  * @work-item-id WI-184
  * @work-item-id WI-189
+ * @work-item-id WI-191
+ * @work-item-id WI-195
+ * @work-item-id WI-196
+ * @work-item-id WI-197
+ * @work-item-id WI-200
  *
  * Phasegate CLI エントリポイント。
  * 各Unitの Composition Root からハンドラーを取得し、コマンドに応じてディスパッチする。
@@ -171,6 +176,7 @@ Commands:
   disable-feature <name>       Disable a harness feature
   list-features                List available features
   migrate                      Migrate phasegate.config.json (--schema v3, --config <path>)
+  migrate work-items           Migrate legacy inception work item directories (--dry-run|--apply)
   work-items:status            Report or apply derived WI frontmatter status (--dry-run|--apply, --id, --fail-on-stale, --json)
 
   render-errors                Render harness errors (--format human|agent|ci)
@@ -211,7 +217,7 @@ Gate semantics:
   refresh-claude-md            Refresh CLAUDE.md standard sections (--dry-run, --apply, --json)
   p2:check-agent-context       Check AGENTS.md / CLAUDE.md freshness (--threshold-days <n>, --json)
   setup:agent                  Plan agent-driven setup (--intent <minimal|recommended|strict|ci-only|agent-hooks|retrofit>, --agent <claude|codex|both>, --dry-run|--apply, --json)
-  config:plan                  Plan safe config changes (--intent <l4-strict|codex-hooks|ci-fail-on-warning|baseline-reset|quick-mode-strict>, --dry-run, --json)
+  config:plan                  Plan safe config changes (--intent <l4-strict|codex-hooks|ci-fail-on-warning|baseline-reset|quick-mode-strict|retrofit-bootstrap|planning-mode-relax>, --dry-run, --json)
   ci:check-repetition          Check error repetition (--code <errorCode>, --reset, --json)
   baseline                     Create retrofit baseline snapshot (--dry-run, --force, --paths <glob,glob,...>, --json)
   scaffold-design              Scaffold a design doc (--unit <id>, --phase <logical|domain|uiux|unit-test|it-test>, --dry-run|--apply, --force, --json)
@@ -528,7 +534,7 @@ Options:
 Produce an agent-readable configuration change plan.
 
 Intents:
-  l4-strict, codex-hooks, ci-fail-on-warning, baseline-reset, quick-mode-strict
+  l4-strict, codex-hooks, ci-fail-on-warning, baseline-reset, quick-mode-strict, retrofit-bootstrap, planning-mode-relax
 
 Options:
   --dry-run
@@ -562,10 +568,11 @@ Options:
   --help, -h                      Show this help`,
   migrate: `Usage: phasegate migrate [options]
 
-Migrate phasegate.config.json from older schema versions. Backs up the original to phasegate.config.json.bak.
+Migrate phasegate.config.json from older schema versions, or migrate legacy inception work item directories.
 
 Options:
   --dry-run                       Preview changes without writing
+  --apply                         Apply migration when supported
   --help, -h                      Show this help`,
   "list-errors": `Usage: phasegate list-errors [options]
 
@@ -769,7 +776,7 @@ function parseCoverageThreshold(raw: string | undefined): number {
 type InitPhasePreset = "full" | "standard" | "minimal" | "custom";
 type AgentTarget = "claude" | "codex" | "both";
 type SetupIntent = "minimal" | "recommended" | "strict" | "ci-only" | "agent-hooks" | "retrofit";
-type ConfigChangeIntent = "l4-strict" | "codex-hooks" | "ci-fail-on-warning" | "baseline-reset" | "quick-mode-strict";
+type ConfigChangeIntent = "l4-strict" | "codex-hooks" | "ci-fail-on-warning" | "baseline-reset" | "quick-mode-strict" | "retrofit-bootstrap" | "planning-mode-relax";
 type SetupCompletenessStatus = "configured" | "planned" | "manual" | "not-applicable" | "unknown";
 
 interface SetupCompletenessEntry {
@@ -847,7 +854,9 @@ function parseConfigChangeIntent(value: string | undefined): ConfigChangeIntent
     value === "codex-hooks" ||
     value === "ci-fail-on-warning" ||
     value === "baseline-reset" ||
-    value === "quick-mode-strict"
+    value === "quick-mode-strict" ||
+    value === "retrofit-bootstrap" ||
+    value === "planning-mode-relax"
   ) {
     return value;
   }
@@ -1216,6 +1225,14 @@ function buildConfigPatchPreview(intent: ConfigChangeIntent, before: unknown | n
     ],
     "codex-hooks": [],
     "baseline-reset": [],
+    "retrofit-bootstrap": [
+      { pointer: "/planningMode/default", path: ["planningMode", "default"], value: "manual" },
+      { pointer: "/phaseDependencies/override", path: ["phaseDependencies", "override"], value: true },
+      { pointer: "/quickMode/relaxedGates", path: ["quickMode", "relaxedGates"], value: ["phase-gate"] },
+    ],
+    "planning-mode-relax": [
+      { pointer: "/planningMode/default", path: ["planningMode", "default"], value: "manual" },
+    ],
   };
   const changes = configIntents[intent];
   if (changes.length === 0) {
@@ -1303,6 +1320,22 @@ async function buildConfigChangePlan(rootDir: string, intent: ConfigChangeIntent
       validations: ["phasegate ci-check --quick --dry-run", "phasegate phasegate:check-ready"],
       risks: ["More changes will require Full Mode validation before commit."],
     },
+    "retrofit-bootstrap": {
+      targets: ["phasegate.config.json: planningMode.default", "phasegate.config.json: phaseDependencies.override", "phasegate.config.json: quickMode.relaxedGates"],
+      managedTargets: ["phasegate.config.json"],
+      externalActions: [],
+      commands: ["phasegate baseline --dry-run", "phasegate config:plan --intent retrofit-bootstrap --json"],
+      validations: ["phasegate validate-metadata docs/inception/_shared/*.md", "phasegate check-phase-gate --level 2"],
+      risks: ["Manual planning mode accepts existing retrofit planning evidence; review the patch before applying it to avoid weakening greenfield projects."],
+    },
+    "planning-mode-relax": {
+      targets: ["phasegate.config.json: planningMode.default"],
+      managedTargets: ["phasegate.config.json"],
+      externalActions: [],
+      commands: ["phasegate config:plan --intent planning-mode-relax --json"],
+      validations: ["phasegate check-phase-gate --level 2", "phasegate phasegate:check-ready"],
+      risks: ["Manual planning mode reduces PhaseGate's QA enforcement for plan documents until strict planning is restored."],
+    },
   };
   const before = await readProjectJson(rootDir, "phasegate.config.json");
   return {
@@ -2371,6 +2404,16 @@ async function main(): Promise<void> {
         break;
       }
 
+      case "status": {
+        console.error("Warning: 'phasegate status' is deprecated; use 'phasegate phasegate:status'.");
+        const mod = createHarnessApiModule();
+        const flags: Record<string, boolean | string> = {};
+        if (json) flags.json = true;
+        await mod.handlers.status.handle({}, flags);
+        if (!json) await printStoryReflectionStatusLine(rootDir);
+        break;
+      }
+
       case "phasegate:lint": {
         const mod = createHarnessApiModule();
         const flags: Record<string, boolean | string> = {};
@@ -2389,6 +2432,15 @@ async function main(): Promise<void> {
         break;
       }
 
+      case "complete-check": {
+        console.error("Warning: 'phasegate complete-check' is deprecated; use 'phasegate phasegate:complete-check'.");
+        const mod = createHarnessApiModule();
+        const flags: Record<string, boolean | string> = {};
+        if (json) flags.json = true;
+        await mod.handlers.completeCheck.handle({}, flags);
+        break;
+      }
+
       case "phasegate:impact-analysis": {
         const mod = createHarnessApiModule();
         const storyId = args[1] && !args[1].startsWith("--") ? args[1] : (parseFlag(args, "--story-id") ?? "");
@@ -2435,6 +2487,11 @@ Examples:
   phasegate ci:generate-template --preset strict --type pre-commit --render`);
           process.exit(0);
         }
+        const flagError = validateKnownFlags(args.slice(1), ["--preset", "--type", "--render", "--json", "--help"]);
+        if (flagError !== null) {
+          console.error(flagError);
+          process.exit(2);
+        }
         const mod = buildCiGovernance(rootDir, harnessRoot);
         const presetId = parseFlag(args, "--preset") ?? "standard";
         const templateType = parseFlag(args, "--type") ?? "aidlc-gate";
@@ -2587,7 +2644,7 @@ Examples:
         const mod = createSkillQualityHandlers();
         const storyId = parseFlag(args, "--story") ?? "";
         const dryRun = hasFlag(args, "--dry-run");
-        const result = await mod.applyCascadeUpdateHandler.handle({ storyId, dryRun });
+        const result = await mod.applyCascadeUpdateHandler.handle({ storyId, dryRun, format: json ? "json" : "human" });
         console.log(result.message);
         process.exit(result.exitCode);
         break;
@@ -2780,6 +2837,10 @@ Examples:
       }
 
       case "delegate-sonnet": {
+        if (hasFlag(args, "--help") || hasFlag(args, "-h")) {
+          printSubcommandHelp("delegate-sonnet");
+          process.exit(0);
+        }
         const { spawn } = await import("node:child_process");
         const scriptPath = join(harnessRoot, "scripts/delegate-sonnet.sh");
         const forwardArgs = args.slice(1);

package/scripts/harness/phase-dependency-model/application/services/phase-info-resolver.ts

@@ -125,7 +125,7 @@ export class PhaseInfoResolver {
           blockers.push(`QAが未完了です: ${node.nodeKey()}`);
         }
         if (!actual.planningModeMatch) {
-          blockers.push(`Planning Mode要件を満たしていません: ${node.nodeKey()}`);
+          blockers.push(`Planning Mode evidence requirement is not satisfied: ${node.nodeKey()}`);
         }
       }
     }

package/scripts/harness/phase-dependency-model/domain/models/phase-structure.ts

@@ -270,7 +270,7 @@ export class PhaseStructure {
         }
 
         if (!planEvidence.planningModeMatch) {
-          blockers.push(`Planning Mode要件を満たしていません: ${node.nodeKey()}`);
+          blockers.push(`Planning Mode evidence requirement is not satisfied: ${node.nodeKey()}`);
         }
       }
 

package/scripts/harness/phase-dependency-model/domain/values/planning-mode.ts

@@ -3,7 +3,7 @@
  * @unit phase-dependency-model
  */
 
-export type PlanningModeValue = 'interactive' | 'embedded-qa';
+export type PlanningModeValue = 'interactive' | 'embedded-qa' | 'manual';
 
 export class InvalidPlanningModeError extends Error {
   constructor(value: string) {
@@ -21,7 +21,7 @@ export class PlanningMode {
   }
 
   static create(value: string): PlanningMode {
-    if (value !== 'interactive' && value !== 'embedded-qa') {
+    if (value !== 'interactive' && value !== 'embedded-qa' && value !== 'manual') {
       throw new InvalidPlanningModeError(value);
     }
 

package/scripts/harness/skill-quality/application/usecases/apply-cascade-update-usecase.ts

@@ -1,6 +1,7 @@
 /**
  * @layer application
  * @unit skill-quality
+ * @work-item-id WI-192
  */
 import { CascadeUpdateResult } from '../../domain/value-objects/cascade-update-result.js';
 import type { CascadeUpdateService } from '../../domain/services/cascade-update-service.js';
@@ -35,7 +36,7 @@ export class ApplyCascadeUpdateUseCase {
             const updatedContent = content.includes(target.storyIdTag)
               ? content
               : `${content}\n${target.storyIdTag}`;
-            if (!input.dryRun) {
+            if (!input.dryRun && updatedContent !== content) {
               await this.fileSystemPort.write(filePath, updatedContent);
             }
             updatedCount++;

package/scripts/harness/skill-quality/presentation/handlers/apply-cascade-update-handler.ts

@@ -1,12 +1,14 @@
 /**
  * @layer presentation
  * @unit skill-quality
+ * @work-item-id WI-192
  */
 import type { ApplyCascadeUpdateUseCase } from '../../application/usecases/apply-cascade-update-usecase.js';
 
 export interface ApplyCascadeUpdateArgs {
   storyId: string;
   dryRun?: boolean;
+  format?: 'human' | 'json';
 }
 
 export class ApplyCascadeUpdateHandler {
@@ -15,8 +17,15 @@ export class ApplyCascadeUpdateHandler {
   async handle(args: ApplyCascadeUpdateArgs): Promise<{ exitCode: number; message: string }> {
     try {
       const output = await this.useCase.execute({ storyId: args.storyId, dryRun: args.dryRun });
+      if (args.format === 'json') {
+        return {
+          exitCode: output.errors.length > 0 ? 1 : 0,
+          message: JSON.stringify({ dryRun: args.dryRun === true, ...output }, null, 2),
+        };
+      }
       const tagsLine = output.appliedStoryIds.join(', ');
-      let msg = `Updated ${output.updatedCount} files with tags: ${tagsLine}`;
+      const verb = args.dryRun ? 'Would update' : 'Updated';
+      let msg = `${verb} ${output.updatedCount} files with tags: ${tagsLine}`;
 
       if (output.errors.length > 0) {
         const errLines = output.errors.map((e) => `  - ${e}`).join('\n');