phasegate 0.335.0 → 0.341.0

package/scripts/harness/agent-integration/application/usecases/handle-pre-tool-use-usecase.ts

@@ -27,6 +27,7 @@ import type {
 } from "../../domain/ports/full-mode-session-query-port.js";
 import type { PhaseGateQueryPort } from "../../domain/ports/phase-gate-query-port.js";
 import type { StoryReflectionQueryPort } from "../../domain/ports/story-reflection-query-port.js";
+import { StoryReflectionQueryResult } from "../../domain/value-objects/story-reflection-query-result.js";
 import { AsyncHookToCliTranslator } from "../../domain/services/hook-to-cli-translator.js";
 import { HookEvent } from "../../domain/value-objects/hook-event.js";
 import type { BlockMetadata } from "../../domain/value-objects/hook-translation-result.js";
@@ -169,8 +170,15 @@ export class HandlePreToolUseUseCase {
             fullModeResult.dominantCategory,
           );
           if (sessionResult.allowed) {
+            const reflection = await this.checkSessionReflection(input, sessionResult);
+            if (reflection.sessionEnforced && !reflection.passed && !reflection.skipped) {
+              const blocked = HandlePreToolUseUseCase.buildStoryReflectionBlockOutput(input.targetFilePaths[0], reflection.blockers, reflection.warnings);
+              return { ...blocked, error: { message: `[L2-STORY-REFLECTION] 明示設定による依存反映チェック\n${reflection.blockers.join('\n')}\n修正方法: inception/productを単独で編集し、必要な上位判断と設計内容を反映してから同じ操作を再評価してください。タグだけでは意味的承認を証明しません。\n依存不明の場合はdescription.mdのID・所属・depends_onを確認してください。` } };
+            }
+            const warnings = [...reflection.blockers, ...reflection.warnings];
             return {
               shouldBlock: false,
+              ...(warnings.length > 0 ? { storyReflectionWarnings: warnings } : {}),
               fullModeSessionAllowed: {
                 workItemId: sessionResult.workItemId,
                 unit: sessionResult.unit,
@@ -187,7 +195,7 @@ export class HandlePreToolUseUseCase {
               input.targetFilePaths[0],
               fullModeResult,
               guidance,
-              unitIdForGuidance,
+              this.deriveRecoveryUnitId(input.targetFilePaths),
               sessionResult,
             );
           }
@@ -225,6 +233,19 @@ export class HandlePreToolUseUseCase {
     );
   }
 
+  private async checkSessionReflection(
+    input: HandlePreToolUseInput,
+    session: FullModeSessionQueryResult,
+  ): Promise<StoryReflectionQueryResult> {
+    if (!session.active || !session.unit || !session.workItemId ||
+      !this.storyReflectionQueryPort?.checkSessionReflection || !this.resolveStoryReflectionScope(input)) return StoryReflectionQueryResult.skipped();
+    try {
+      return await this.storyReflectionQueryPort.checkSessionReflection(session.unit, session.workItemId);
+    } catch (error) {
+      return StoryReflectionQueryResult.skipped([`WI依存反映は未検証です（既存sessionの許可を維持）: ${error instanceof Error ? error.message : String(error)}`]);
+    }
+  }
+
   private async checkGrandfather(targetFilePaths: readonly string[]): Promise<BaselineGrandfatherCheckResult> {
     if (this.baselineGrandfatherQueryPort === undefined) {
       return {
@@ -278,7 +299,7 @@ export class HandlePreToolUseUseCase {
     blockedFilePath: string | undefined,
     result: {
       requiresFullMode: boolean;
-      rejectionRule?: "MIXED_CHANGES" | "NEW_DOMAIN" | "API_CONTRACT";
+      rejectionRule?: "CATEGORY_NOT_ALLOWED" | "MIXED_CHANGES" | "NEW_DOMAIN" | "API_CONTRACT";
       rejectionReason?: string;
       dominantCategory?: string;
     },
@@ -352,6 +373,7 @@ export class HandlePreToolUseUseCase {
     HandlePreToolUseUseCase.appendJudgmentContextLines(lines, sessionResult);
     const suggestedSkill = guidance?.suggestedSkill ?? "/story-implementor";
     lines.push(`次のアクション: ${suggestedSkill} スキルを使用して設計フェーズから開始してください。`);
+    lines.push('  inceptionの計画編集と実装を分け、実装は対象Unitごとに設計反映とsession開始を行ってください。');
     if (unitId !== undefined && unitId !== "") {
       if (HandlePreToolUseUseCase.isSessionActiveButRejected(sessionResult)) {
         lines.push(
@@ -362,6 +384,8 @@ export class HandlePreToolUseUseCase {
         `  実装フェーズ開始時: phasegate session begin --mode full --unit ${unitId} --work-item <WI-XXX> --reason "<reason>" --duration 1h`,
       );
       lines.push("  実装完了時: phasegate session end --work-item <WI-XXX>");
+    } else {
+      lines.push('  対象Unitが一意に決まりません。実装対象パスのUnitを確認してください（_crossはsessionのUnitに指定できません）。');
     }
     HandlePreToolUseUseCase.appendGuidanceLines(lines, guidance, unitId);
 
@@ -458,6 +482,17 @@ export class HandlePreToolUseUseCase {
     return `${templatePath}（未配置なら: npx phasegate skills info ${skillMatch[1]}）`;
   }
 
+  private deriveRecoveryUnitId(targetFilePaths: readonly string[]): string | undefined {
+    const projectPaths = this.configQueryPort.getProjectPaths();
+    const units = new Set<string>();
+    for (const targetFilePath of targetFilePaths) {
+      if (HandlePreToolUseUseCase.isUnderInception(targetFilePath, projectPaths.getDocsInception())) continue;
+      const unit = WriteTargetScope.fromPath(targetFilePath, projectPaths)?.unitId;
+      if (unit !== undefined && /^[A-Za-z0-9][A-Za-z0-9_-]*$/.test(unit)) units.add(unit);
+    }
+    return units.size === 1 ? [...units][0] : undefined;
+  }
+
   private deriveUnitIdFromPaths(targetFilePaths: readonly string[]): string | undefined {
     const projectPaths = this.configQueryPort.getProjectPaths();
     for (const targetFilePath of targetFilePaths) {
@@ -581,7 +616,7 @@ export class HandlePreToolUseUseCase {
       // WI-363: .husky/ 配下は L0 runtime の実施点。Quick Mode でも書き換えさせない。
       pattern: /(?:^|\/)\.husky\//,
       message: (fp) =>
-        `保護ファイルへの書き込みがブロックされました: ${fp}\n.husky/ 配下は L0 runtime（pre-commit / commit-msg / pre-push）の実施点であり、Quick Mode でも変更できません。\n未導入 hook の配置は npx phasegate setup:agent --apply --with-husky を使用してください。\n意図的に手編集する場合は phasegate.config.json の protectedFiles.exclude に対象パターンを明示してください。`,
+        `保護ファイルへの書き込みがブロックされました: ${fp}\n.husky/ 配下は L0 runtime（pre-commit / commit-msg / pre-push）の実施点であり、Quick Mode でも変更できません。\n未導入 hook の配置は npx phasegate setup:agent --apply --with-husky を使用してください。\n意図的な手編集が必要な場合は、agent セッション外で人間が変更し、通常の検証を実行してください。`,
     },
   ];
 

package/scripts/harness/agent-integration/application/usecases/handle-stop-usecase.ts

@@ -2,14 +2,12 @@
  * @layer application
  * @unit agent-integration
  * @story H11-04
+ * @work-item-id WI-220
  *
  * HandleStopUseCase
  * Stop Hook処理のオーケストレーション。ReentryGuardライフサイクル管理の唯一の制御点
  */
 
-import { HookEvent } from '../../domain/value-objects/hook-event.js';
-import { ReentryGuard } from '../../domain/entities/reentry-guard.js';
-import { AsyncHookToCliTranslator } from '../../domain/services/hook-to-cli-translator.js';
 import type { ReentryGuardStatePort } from '../../domain/ports/reentry-guard-state-port.js';
 import type { ConfigQueryPort } from '../../domain/ports/config-query-port.js';
 import type { CliExecutorPort } from '../ports/cli-executor-port.js';
@@ -19,7 +17,8 @@ export interface HandleStopUseCasePorts {
   reentryGuardStatePort: ReentryGuardStatePort;
   cliExecutorPort: CliExecutorPort;
   configQueryPort: ConfigQueryPort;
-  cliCommandRegistryPort: {
+  /** Legacy constructor input; Stop dispatches complete-check directly. */
+  cliCommandRegistryPort?: {
     hasCommand(commandName: string): Promise<boolean>;
     listCommands(): Promise<readonly string[]>;
   };
@@ -37,16 +36,11 @@ export class HandleStopUseCase {
   private readonly reentryGuardStatePort: ReentryGuardStatePort;
   private readonly cliExecutorPort: CliExecutorPort;
   private readonly configQueryPort: ConfigQueryPort;
-  private readonly cliCommandRegistryPort: {
-    hasCommand(commandName: string): Promise<boolean>;
-    listCommands(): Promise<readonly string[]>;
-  };
 
   constructor(ports: HandleStopUseCasePorts) {
     this.reentryGuardStatePort = ports.reentryGuardStatePort;
     this.cliExecutorPort = ports.cliExecutorPort;
     this.configQueryPort = ports.configQueryPort;
-    this.cliCommandRegistryPort = ports.cliCommandRegistryPort;
   }
 
   async execute(input: HandleStopInput): Promise<HandleStopOutput> {

package/scripts/harness/agent-integration/domain/ports/full-mode-requirement-query-port.ts

@@ -1,15 +1,17 @@
 // @unit agent-integration
 // @layer domain
+// @work-item-id WI-384
 
 export interface FullModeRequirementQueryResult {
   readonly requiresFullMode: boolean;
-  readonly rejectionRule?: 'MIXED_CHANGES' | 'NEW_DOMAIN' | 'API_CONTRACT';
+  readonly rejectionRule?: 'CATEGORY_NOT_ALLOWED' | 'MIXED_CHANGES' | 'NEW_DOMAIN' | 'API_CONTRACT';
   readonly rejectionReason?: string;
   readonly dominantCategory?: string;
 }
 
 export interface FullModeTargetChange {
   readonly filePath: string;
+  readonly changeKind?: 'CREATE' | 'MODIFY' | 'DELETE';
   readonly beforeContent?: string | null;
   readonly afterContent?: string | null;
 }

package/scripts/harness/agent-integration/domain/ports/story-reflection-query-port.ts

@@ -5,4 +5,6 @@ import type { StoryReflectionQueryResult } from '../value-objects/story-reflecti
 
 export interface StoryReflectionQueryPort {
   checkReflection(unitId: string): Promise<StoryReflectionQueryResult>;
+  /** WI-220: optional session path, advisory by default; caller supplies authenticated identity. */
+  checkSessionReflection?(unitId: string, workItemId: string): Promise<StoryReflectionQueryResult>;
 }

package/scripts/harness/agent-integration/domain/services/apply-patch-write-target-extractor.ts

@@ -0,0 +1,98 @@
+/**
+ * @layer domain
+ * @unit agent-integration
+ * @work-item-id WI-384
+ *
+ * Codex apply_patch の raw patch から書き込み対象と変更種別を抽出する。
+ */
+
+export type PatchChangeKind = "CREATE" | "MODIFY" | "DELETE";
+
+export interface PatchWriteTarget {
+  readonly filePath: string;
+  readonly changeKind: PatchChangeKind;
+}
+
+const APPLY_PATCH_BEGIN_SOURCE = String.raw`\*\*\*\s+Begin\s+Patch`;
+const APPLY_PATCH_END_SOURCE = String.raw`\*\*\*\s+End\s+Patch`;
+const APPLY_PATCH_FILE_LINE_SOURCE = String.raw`^\*\*\*\s+(Update|Add|Delete)\s+File:\s*(.+?)\s*$`;
+const APPLY_PATCH_MOVE_LINE_SOURCE = String.raw`^\*\*\*\s+Move\s+to:\s*(.+?)\s*$`;
+
+const CHANGE_KIND_BY_DIRECTIVE = Object.freeze({
+  Add: "CREATE",
+  Update: "MODIFY",
+  Delete: "DELETE",
+} as const satisfies Readonly<Record<string, PatchChangeKind>>);
+
+const EMPTY_TARGETS: readonly PatchWriteTarget[] = Object.freeze([]);
+
+export class ApplyPatchWriteTargetExtractor {
+  extract(rawPatch: string): readonly PatchWriteTarget[] {
+    if (typeof rawPatch !== "string" || rawPatch.length === 0) {
+      return EMPTY_TARGETS;
+    }
+
+    const beginGlobal = new RegExp(APPLY_PATCH_BEGIN_SOURCE, "g");
+    const beginStarts: number[] = [];
+    let match = beginGlobal.exec(rawPatch);
+    while (match !== null) {
+      beginStarts.push(match.index + match[0].length);
+      match = beginGlobal.exec(rawPatch);
+    }
+    if (beginStarts.length === 0) {
+      return EMPTY_TARGETS;
+    }
+
+    const endGlobal = new RegExp(APPLY_PATCH_END_SOURCE, "g");
+    const endStarts: number[] = [];
+    match = endGlobal.exec(rawPatch);
+    while (match !== null) {
+      endStarts.push(match.index);
+      match = endGlobal.exec(rawPatch);
+    }
+
+    const targets: PatchWriteTarget[] = [];
+    const seen = new Set<string>();
+    for (let index = 0; index < beginStarts.length; index += 1) {
+      const start = beginStarts[index];
+      const nextBegin = index + 1 < beginStarts.length ? beginStarts[index + 1] : rawPatch.length;
+      const endInRange = endStarts.find((candidate) => candidate > start && candidate <= nextBegin);
+      const body = rawPatch.slice(start, endInRange ?? nextBegin);
+      let acceptsMoveDestination = false;
+
+      for (const line of body.split(/\r?\n/)) {
+        const fileMatch = new RegExp(APPLY_PATCH_FILE_LINE_SOURCE).exec(line);
+        if (fileMatch !== null) {
+          const directive = fileMatch[1] as keyof typeof CHANGE_KIND_BY_DIRECTIVE;
+          const filePath = fileMatch[2].trim();
+          acceptsMoveDestination = directive === "Update";
+          if (filePath.length === 0) continue;
+          const changeKind = CHANGE_KIND_BY_DIRECTIVE[directive];
+          this.appendTarget(targets, seen, filePath, changeKind);
+          continue;
+        }
+
+        const moveMatch = acceptsMoveDestination ? new RegExp(APPLY_PATCH_MOVE_LINE_SOURCE).exec(line) : null;
+        acceptsMoveDestination = false;
+        if (moveMatch === null) continue;
+        const filePath = moveMatch[1].trim();
+        if (filePath.length === 0) continue;
+        this.appendTarget(targets, seen, filePath, "CREATE");
+      }
+    }
+
+    return targets.length === 0 ? EMPTY_TARGETS : Object.freeze(targets);
+  }
+
+  private appendTarget(
+    targets: PatchWriteTarget[],
+    seen: Set<string>,
+    filePath: string,
+    changeKind: PatchChangeKind,
+  ): void {
+    const key = `${changeKind}\u0000${filePath}`;
+    if (seen.has(key)) return;
+    seen.add(key);
+    targets.push(Object.freeze({ filePath, changeKind }));
+  }
+}

package/scripts/harness/agent-integration/domain/services/bash-write-target-extractor.ts

@@ -1,6 +1,7 @@
 /**
  * @layer domain
  * @unit agent-integration
+ * @work-item-id WI-384
  *
  * BashWriteTargetExtractor ドメインサービス
  *
@@ -25,6 +26,8 @@
  *     `*** Update|Add|Delete File: <path>` 行) — Codex CLI 対応 (ISSUE-013 Wave 1)
  */
 
+import { ApplyPatchWriteTargetExtractor } from './apply-patch-write-target-extractor.js';
+
 /** 引数トークン (値とクォート種別) */
 type Token = {
   readonly value: string;
@@ -508,62 +511,13 @@ function extractFromCommandString(command: string): string[] {
     }
   }
   // ネスト内の apply_patch heredoc も拾う
-  for (const p of extractApplyPatchTargets(command)) {
-    collected.push(p);
+  const patchExtractor = new ApplyPatchWriteTargetExtractor();
+  for (const target of patchExtractor.extract(command)) {
+    collected.push(target.filePath);
   }
   return collected;
 }
 
-/** apply_patch ブロック境界マーカー (Begin/End) */
-const APPLY_PATCH_BEGIN_SOURCE = String.raw`\*\*\*\s+Begin\s+Patch`;
-const APPLY_PATCH_END_SOURCE = String.raw`\*\*\*\s+End\s+Patch`;
-/** ブロック内のファイル行: `*** (Update|Add|Delete) File: <path>` */
-const APPLY_PATCH_FILE_LINE_SOURCE = String.raw`^\s*\*\*\*\s+(?:Update|Add|Delete)\s+File:\s*(.+?)\s*$`;
-
-/**
- * apply_patch ヒアドキュメント構文から対象ファイルパスを抽出する。
- *
- * Codex CLI 等が採用する unified-diff 風パッチフォーマット:
- *   *** Begin Patch
- *   *** Update File: <path>
- *   *** Add File: <path>
- *   *** Delete File: <path>
- *   *** End Patch
- *
- * `*** End Patch` が欠けている場合は command 末尾までをブロックとして扱う
- * (保護側に倒す — phase-gate の取りこぼしよりも誤検出のほうが許容される)。
- */
-function extractApplyPatchTargets(command: string): string[] {
-  const beginGlobal = new RegExp(APPLY_PATCH_BEGIN_SOURCE, 'g');
-  const beginStarts: number[] = [];
-  let m: RegExpExecArray | null;
-  while ((m = beginGlobal.exec(command)) !== null) {
-    beginStarts.push(m.index + m[0].length);
-  }
-  if (beginStarts.length === 0) return [];
-
-  const endGlobal = new RegExp(APPLY_PATCH_END_SOURCE, 'g');
-  const endStarts: number[] = [];
-  while ((m = endGlobal.exec(command)) !== null) {
-    endStarts.push(m.index);
-  }
-
-  const results: string[] = [];
-  for (let i = 0; i < beginStarts.length; i += 1) {
-    const start = beginStarts[i];
-    const nextBegin = i + 1 < beginStarts.length ? beginStarts[i + 1] : command.length;
-    const endInRange = endStarts.find((e) => e > start && e <= nextBegin);
-    const end = endInRange ?? nextBegin;
-    const body = command.slice(start, end);
-
-    const fileRegex = new RegExp(APPLY_PATCH_FILE_LINE_SOURCE, 'gm');
-    while ((m = fileRegex.exec(body)) !== null) {
-      results.push(m[1]);
-    }
-  }
-  return results;
-}
-
 export class BashWriteTargetExtractor {
   /**
    * Bash コマンド文字列から書き込み先ファイルパスを抽出する。

package/scripts/harness/agent-integration/domain/services/hook-to-cli-translator.ts

@@ -140,7 +140,7 @@ export class HookToCliTranslator {
       throw new CommandNotRegisteredError(commandName);
     }
 
-    return HookTranslationResult.execute(commandName, ['--fast'], 0, 500);
+    return HookTranslationResult.execute(commandName, [...new Set(event.affectedFilePaths)].flatMap((target) => ['--target', target]), 0, 5000);
   }
 
   private translateStop(_event: StopEvent): HookTranslationResult {
@@ -248,7 +248,10 @@ export class AsyncHookToCliTranslator {
     const projectPaths = await (this.configQueryPort as ConfigQueryPort & {
       getProjectPaths(): unknown;
     }).getProjectPaths();
-    const detectedScope = event.targetFilePaths
+    const gatePaths = event.targetFilePaths.filter(filePath => !WriteTargetScope.isInceptionDocument(
+      filePath, projectPaths as Parameters<typeof WriteTargetScope.fromPath>[1],
+    ));
+    const detectedScope = gatePaths
       .map((filePath) => WriteTargetScope.fromPath(filePath, projectPaths as Parameters<typeof WriteTargetScope.fromPath>[1]))
       .find((scope): scope is WriteTargetScope => scope !== null);
 
@@ -272,7 +275,7 @@ export class AsyncHookToCliTranslator {
 
     const phaseGateResult = await this.phaseGateQueryPort.checkGate(
       detectedScope,
-      event.targetFilePaths[0],
+      gatePaths.find(filePath => WriteTargetScope.fromPath(filePath, projectPaths as Parameters<typeof WriteTargetScope.fromPath>[1]) !== null),
     );
     if (!phaseGateResult.hasPassed()) {
       return HookTranslationResult.block({
@@ -292,7 +295,7 @@ export class AsyncHookToCliTranslator {
     });
   }
 
-  private async translatePostToolUse(_event: PostToolUseEvent): Promise<HookTranslationResult> {
+  private async translatePostToolUse(event: PostToolUseEvent): Promise<HookTranslationResult> {
     const isEnabled = await this.configQueryPort.isHookEnabled('post-tool-use');
     if (!isEnabled) {
       return HookTranslationResult.skip('HOOK_DISABLED');
@@ -304,7 +307,7 @@ export class AsyncHookToCliTranslator {
       throw new CommandNotRegisteredError(commandName);
     }
 
-    return HookTranslationResult.execute(commandName, ['--fast'], 0, 500);
+    return HookTranslationResult.execute(commandName, [...new Set(event.affectedFilePaths)].flatMap((target) => ['--target', target]), 0, 5000);
   }
 
   private async translateStop(_event: StopEvent): Promise<HookTranslationResult> {

package/scripts/harness/agent-integration/domain/value-objects/hook-translation-result.ts

@@ -6,7 +6,7 @@
  * HookEvent → CLI実行指示への変換結果
  */
 
-export type SkipReason = 'REENTRY_DETECTED' | 'HOOK_DISABLED' | 'TIMEOUT_EXCEEDED';
+export type SkipReason = 'REENTRY_DETECTED' | 'HOOK_DISABLED' | 'TIMEOUT_EXCEEDED' | 'READ_ONLY';
 
 export type BlockReason = 'PROTECTED_FILE' | 'PHASE_GATE' | 'FULL_MODE_REQUIRED';
 
@@ -18,7 +18,7 @@ export interface BlockMetadata {
   readonly scopeLevel?: 1 | 2 | 3;
   readonly unitId?: string;
   readonly storyId?: string;
-  readonly fullModeRejectionRule?: 'MIXED_CHANGES' | 'NEW_DOMAIN' | 'API_CONTRACT';
+  readonly fullModeRejectionRule?: 'CATEGORY_NOT_ALLOWED' | 'MIXED_CHANGES' | 'NEW_DOMAIN' | 'API_CONTRACT';
   readonly fullModeRejectionReason?: string;
   readonly fullModeDominantCategory?: string;
 }

package/scripts/harness/agent-integration/domain/value-objects/protected-file-list.ts

@@ -1,6 +1,7 @@
 /**
  * @layer domain
  * @unit agent-integration
+ * @work-item-id WI-390
  *
  * ProtectedFileList 値オブジェクト
  * 変更をブロックすべきファイルのパターンリスト
@@ -14,13 +15,15 @@ export class ProtectedFileListEmptyError extends Error {
   }
 }
 
-/** デフォルトの保護対象ファイルパターン */
-const DEFAULT_PATTERNS = [
-  'biome.json',
-  '.biome.json',
-  'tsconfig.json',
-  'package.json',
-  'package-lock.json',
+/**
+ * 設定から除外できない agent trust roots。
+ * これらを protectedFiles.exclude で解除できると、防御機構そのものを agent が
+ * 無効化してから書き換えられるため、通常の保護対象とは別の集合で保持する。
+ */
+const NON_EXCLUDABLE_PATTERNS = [
+  'phasegate.config.json',
+  '.phasegate-local/phasegate.config.json',
+  '**/phasegate.config.json',
   // baseline.json は grandfather 判定の信頼基盤。手動追記による protected file の
   // grandfather bypass を防ぐため、書き込み自体を保護対象とする。
   '.phasegate/baseline.json',
@@ -30,8 +33,24 @@ const DEFAULT_PATTERNS = [
   // 入ったため、防御機構そのものの書き換えを protected file として明示的に止める。
   '.husky/**',
   '**/.husky/**',
+  // Root agent instructions determine the permissions and operating procedure
+  // used by coding agents, so direct agent writes must remain blocked.
+  'CLAUDE.md',
+  'AGENTS.md',
+  'GEMINI.md',
+];
+
+/** 利用者設定で除外可能な通常のデフォルト保護対象。 */
+const EXCLUDABLE_DEFAULT_PATTERNS = [
+  'biome.json',
+  '.biome.json',
+  'tsconfig.json',
+  'package.json',
+  'package-lock.json',
 ];
 
+const DEFAULT_PATTERNS = [...NON_EXCLUDABLE_PATTERNS, ...EXCLUDABLE_DEFAULT_PATTERNS];
+
 /**
  * glob パターンのシンプルなマッチング実装
  * micromatch なしで基本的な glob をサポート
@@ -79,23 +98,21 @@ export class ProtectedFileList {
   }
 
   static createWithExclusions(exclusions: string[]): ProtectedFileList {
-    const filtered = DEFAULT_PATTERNS.filter((p) => !exclusions.includes(p));
-    if (filtered.length === 0) {
-      return new ProtectedFileList([...DEFAULT_PATTERNS]);
-    }
-    return new ProtectedFileList(filtered);
+    const excludable = EXCLUDABLE_DEFAULT_PATTERNS.filter((p) => !exclusions.includes(p));
+    return new ProtectedFileList([...NON_EXCLUDABLE_PATTERNS, ...excludable]);
   }
 
   static createWithAdditionalAndExclusions(
     additionalPatterns: string[],
     exclusions: string[],
   ): ProtectedFileList {
-    const base = DEFAULT_PATTERNS.filter((p) => !exclusions.includes(p));
-    const allPatterns = [...base, ...additionalPatterns];
-    if (allPatterns.length === 0) {
-      return new ProtectedFileList([...DEFAULT_PATTERNS]);
-    }
-    return new ProtectedFileList(allPatterns);
+    const excludableDefaults = EXCLUDABLE_DEFAULT_PATTERNS.filter((p) => !exclusions.includes(p));
+    const excludableAdditional = additionalPatterns.filter((p) => !exclusions.includes(p));
+    return new ProtectedFileList([
+      ...NON_EXCLUDABLE_PATTERNS,
+      ...excludableDefaults,
+      ...excludableAdditional,
+    ]);
   }
 
   matches(filePath: string): boolean {

package/scripts/harness/agent-integration/domain/value-objects/story-reflection-query-result.ts

@@ -14,6 +14,7 @@ export class StoryReflectionQueryResult {
   readonly blockers: readonly string[];
   readonly warnings: readonly string[];
   readonly skipped: boolean;
+  declare readonly sessionEnforced?: true;
 
   private constructor(
     passed: boolean,
@@ -27,8 +28,8 @@ export class StoryReflectionQueryResult {
     this.skipped = skipped;
   }
 
-  static pass(): StoryReflectionQueryResult {
-    return new StoryReflectionQueryResult(true, [], [], false);
+  static pass(warnings: string[] = []): StoryReflectionQueryResult {
+    return new StoryReflectionQueryResult(true, [], warnings, false);
   }
 
   static skipped(warnings: string[] = []): StoryReflectionQueryResult {
@@ -45,6 +46,13 @@ export class StoryReflectionQueryResult {
     return new StoryReflectionQueryResult(false, blockers, warnings, false);
   }
 
+  /** Only trusted configuration readers may mark the optional session enforcement path. */
+  withSessionEnforcement(): StoryReflectionQueryResult {
+    return Object.assign(new StoryReflectionQueryResult(this.passed, this.blockers, this.warnings, this.skipped), {
+      sessionEnforced: true as const,
+    });
+  }
+
   hasPassed(): boolean {
     return this.passed;
   }

package/scripts/harness/agent-integration/domain/value-objects/write-target-scope.ts

@@ -61,6 +61,9 @@ export class WriteTargetScope {
       if (sourceMatch !== null) {
         const [unitId] = sourceMatch;
         if (unitId !== undefined) {
+          // A source-root file (e.g. main.ts) is not a Unit directory.
+          // Keep nested paths, including dotted directory names, under the gate.
+          if (sourceMatch.length === 1 && unitId.includes('.')) continue;
           return WriteTargetScope.create({ level: 3, unitId });
         }
       }
@@ -124,6 +127,15 @@ export class WriteTargetScope {
     return null;
   }
 
+  /** Phase-1 Markdown repair is not implementation; source-root overlaps remain gated. */
+  static isInceptionDocument(filePath: string, projectPaths: ProjectPaths): boolean {
+    const normalized = normalize(filePath);
+    return normalized.toLowerCase().endsWith('.md')
+      && matchPrefix(normalized, projectPaths.getDocsInception()) !== null
+      && !projectPaths.getSource().some(root => matchPrefix(normalized, root) !== null)
+      && WriteTargetScope.fromPath(normalized, projectPaths)?.level === 3;
+  }
+
   equals(other: WriteTargetScope): boolean {
     return this.level === other.level && this.unitId === other.unitId && this.storyId === other.storyId;
   }