scene-capability-engine 3.6.38 → 3.6.39

package/CHANGELOG.md

@@ -7,6 +7,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [3.6.39] - 2026-03-13
+
+### Added
+- Added state storage tiering policy artifacts and guidance in `docs/state-storage-tiering.md`, `docs/state-migration-reconciliation-runbook.md`, `.sce/config/state-storage-policy.json`, and `template/.sce/config/state-storage-policy.json`.
+- Added append-only evidence projection and audit tooling via `scripts/interactive-approval-event-projection.js`, `scripts/state-storage-tiering-audit.js`, and the `audit:state-storage` / `report:state-storage` package scripts.
+- Added scene command coverage and helper fixtures for the expanded `scene` subcommand surface, including publish/install/info/diff/validate/owner/tag/stats/lock/contribute/version and related property tests.
+- Added release-facing closeout evidence for the scene command specs and the quality hardening master spec under `.sce/specs/*/custom/`.
+
+### Changed
+- Expanded `lib/commands/scene.js` to cover the newer scene command flows and stabilized JSON summary output so CLI JSON mode preserves edge-case numeric payloads such as `-0`.
+- Hardened state migration and storage behavior in `lib/state/sce-state-store.js`, `lib/state/state-migration-manager.js`, `lib/runtime/session-store.js`, and related governance/config plumbing while keeping file sources canonical.
+- Completed the `115-00-sce-quality-hardening-program` integration closeout, including `watch logs --follow` completion, open-handle governance follow-through, and master/sub-spec status convergence.
+- Updated `docs/command-reference.md`, `docs/document-governance.md`, and multiple Spec task ledgers to reflect the shipped command surface and governance posture.
+
+### Fixed
+- Removed the remaining `forceExit` dependency from the validated Jest path and confirmed `npm run test:handles` passes without open-handle leakage.
+- Stabilized watch/integration helper timing and watcher cleanup paths so `test:smoke`, `test:full`, and `test:handles` can run cleanly in sequence.
+
 ## [3.6.38] - 2026-03-12
 
 ### Added

package/docs/command-reference.md

@@ -876,6 +876,29 @@ Runtime read preference:
 - `sce state doctor --json` now includes:
   - `summary` aggregate (`pending_components`, `total_record_drift`, `blocking_count`, `alert_count`)
   - runtime read diagnostics (`runtime.timeline`, `runtime.scene_session`) with read-source/read-preference and consistency status
+  - hardened severity model:
+    - `blocking`: `sqlite-unavailable`, `source-parse-error`, `sqlite-ahead`, `sqlite-only`
+    - `alert`: `pending-migration`, `missing-source`, runtime `pending-sync`
+  - current release guidance:
+    - treat `sqlite-ahead` and `sqlite-only` as anomalies requiring repair before release
+    - treat `pending-migration` as repairable drift, not a steady-state
+    - only allow `missing-source` to persist when the component is intentionally out of scope for the project
+
+State storage tiering policy:
+- Policy file: `.sce/config/state-storage-policy.json`
+- Audit command: `npm run audit:state-storage`
+- Machine-readable report: `npm run report:state-storage`
+- Tier meanings:
+  - `file-source`: canonical evidence, audit, recovery payloads, and low-cardinality personal state
+  - `sqlite-index`: query-oriented registry/index layer with files still canonical
+  - `derived-sqlite-projection`: rebuildable SQLite projection for append-only stream queries
+- Explicit non-candidates for SQLite source replacement:
+  - `~/.sce/workspace-state.json`
+  - `.sce/reports/**/*.jsonl`
+  - `.sce/audit/**/*.jsonl`
+- Supporting docs:
+  - `docs/state-storage-tiering.md`
+  - `docs/state-migration-reconciliation-runbook.md`
 
 Write lease model (optional, policy-driven, SQLite-backed):
 - Policy file: `.sce/config/authorization-policy.json`
@@ -1836,6 +1859,10 @@ Interactive approval workflow helper (script-level stage-B approval state machin
 - `node scripts/interactive-approval-workflow.js --action <init|submit|approve|reject|execute|verify|archive|status> [--plan <path>] [--state-file <path>] [--audit-file <path>] [--actor <id>] [--actor-role <name>] [--role-policy <path>] [--comment <text>] [--password <text>] [--password-hash <sha256>] [--password-hash-env <name>] [--password-required] [--password-scope <csv>] [--json]`: maintain approval lifecycle state for interactive change plans and append approval events to JSONL audit logs.
   - Default state file: `.sce/reports/interactive-approval-state.json`
   - Default audit file: `.sce/reports/interactive-approval-events.jsonl`
+- `node scripts/interactive-approval-event-projection.js --action <rebuild|doctor|query> [--input <path>] [--read-source <auto|file|projection>] [--workflow-id <id>] [--actor <id>] [--approval-action <name>] [--event-type <type>] [--blocked|--not-blocked] [--limit <n>] [--fail-on-drift] [--fail-on-parse-error] [--json]`: build and inspect a rebuildable SQLite projection for `interactive-approval-events.jsonl` while keeping raw JSONL as canonical evidence.
+  - `rebuild` clears and rebuilds the projection for the target audit file
+  - `doctor` compares raw file count vs projection count and flags `projection-missing`, `pending-projection`, `projection-ahead`, or parse errors
+  - `query` discloses `read_source=file|projection`
   - `init` requires `--plan`; high-risk plans are marked as `approval_required=true`.
   - Password authorization can be required per plan (`plan.authorization.password_required=true`) or overridden in `init`.
   - `execute` is blocked (exit code `2`) when approval is required but current status is not `approved`.

package/docs/document-governance.md

@@ -21,7 +21,7 @@ Document governance ensures your project follows these rules:
 
 1. **Root Directory** - Only 4 markdown files allowed: `README.md`, `README.zh.md`, `CHANGELOG.md`, `CONTRIBUTING.md`
 2. **Spec Structure** - Each Spec must have `requirements.md`, `design.md`, `tasks.md`
-3. **Artifact Organization** - Spec artifacts must be in subdirectories: `reports/`, `scripts/`, `tests/`, `results/`, `docs/`
+3. **Artifact Organization** - Spec artifacts must be in subdirectories, except approved Spec-root metadata such as `requirements.md`, `design.md`, `tasks.md`, and `collaboration.json`
 4. **No Temporary Files** - Temporary documents (like `*-SUMMARY.md`, `SESSION-*.md`) must be deleted after use
 
 ### Why Use Document Governance?
@@ -128,7 +128,7 @@ sce docs diagnose
 - Root directory for non-allowed markdown files
 - Root directory for temporary documents
 - Spec directories for missing required files
-- Spec directories for misplaced artifacts
+- Spec directories for misplaced artifacts outside approved Spec-root metadata
 - Spec directories for temporary documents
 
 **Output:**
@@ -240,6 +240,7 @@ sce docs validate [options]
 **What it validates:**
 - Root directory has only allowed markdown files
 - Spec directories have required files (requirements.md, design.md, tasks.md)
+- Spec root contains only approved metadata files plus governed subdirectories
 - Spec subdirectories follow naming conventions
 - No misplaced artifacts
 
@@ -443,6 +444,7 @@ sce docs config [options]
 
 **Configuration keys:**
 - `root-allowed-files` - Allowed markdown files in root
+- `spec-allowed-root-files` - Allowed files at Spec root before artifact warnings apply
 - `spec-subdirs` - Recognized Spec subdirectories
 - `temporary-patterns` - Patterns for temporary files
 
@@ -467,6 +469,12 @@ Spec Subdirectories:
   • results
   • docs
 
+Spec Allowed Root Files:
+  • requirements.md
+  • design.md
+  • tasks.md
+  • collaboration.json
+
 Temporary Patterns:
   • *-SUMMARY.md
   • SESSION-*.md
@@ -724,6 +732,12 @@ The default configuration is:
     "CHANGELOG.md",
     "CONTRIBUTING.md"
   ],
+  "specAllowedRootFiles": [
+    "requirements.md",
+    "design.md",
+    "tasks.md",
+    "collaboration.json"
+  ],
   "specSubdirs": [
     "reports",
     "scripts",
@@ -749,6 +763,11 @@ The default configuration is:
 sce docs config --set root-allowed-files "README.md,README.zh.md,CHANGELOG.md,CONTRIBUTING.md,LICENSE.md,SECURITY.md"
 ```
 
+**Allow additional Spec-root metadata:**
+```bash
+sce docs config --set spec-allowed-root-files "requirements.md,design.md,tasks.md,collaboration.json"
+```
+
 **Add custom subdirectories:**
 ```bash
 sce docs config --set spec-subdirs "reports,scripts,tests,results,docs,diagrams,examples"
@@ -768,6 +787,7 @@ You can also edit this file directly:
 ```json
 {
   "rootAllowedFiles": ["README.md", "CUSTOM.md"],
+  "specAllowedRootFiles": ["requirements.md", "design.md", "tasks.md", "collaboration.json"],
   "specSubdirs": ["reports", "scripts", "custom"],
   "temporaryPatterns": ["*-TEMP.md"]
 }

package/docs/releases/README.md

@@ -9,6 +9,7 @@ This directory stores release-facing documents:
 ## Archived Versions
 
 - [Release checklist](../release-checklist.md)
+- [v3.6.39 release notes](./v3.6.39.md)
 - [v3.6.38 release notes](./v3.6.38.md)
 - [v3.6.37 release notes](./v3.6.37.md)
 - [v1.46.2 release notes](./v1.46.2.md) (historical)

package/docs/releases/v3.6.39.md

@@ -0,0 +1,24 @@
+# v3.6.39 Release Notes
+
+Release date: 2026-03-13
+
+## Highlights
+
+- Added a canonical state-storage tiering policy, reconciliation runbook, and audit/report tooling so SQLite remains a scoped index layer rather than a silent source-of-truth replacement.
+- Expanded and hardened the `sce scene` command surface with broader command coverage, stronger property tests, and JSON summary output that preserves edge-case numeric payloads.
+- Closed the `115-00-sce-quality-hardening-program` integration loop, including `watch logs --follow` completion and Jest open-handle governance without relying on `forceExit`.
+
+## Verification
+
+- `node bin/sce.js collab status 115-00-sce-quality-hardening-program --graph`
+- `npm run test:smoke`
+- `npm run test:skip-audit`
+- `npm run test:brand-consistency`
+- `npm run test:full`
+- `npm run test:handles`
+
+## Release Notes
+
+- State persistence is now explicitly tiered: evidence and operator-facing files remain canonical, while SQLite stays limited to rebuildable index/projection use cases.
+- The scene command family is substantially more release-ready, with dedicated tests and closeout artifacts across publish/install/info/diff/validate/owner/tag/stats/lock/contribute/version flows.
+- Quality hardening gates should be executed in sequence for release validation; `test:full` and `test:handles` are both green when run serially.

package/docs/state-migration-reconciliation-runbook.md

@@ -0,0 +1,76 @@
+# State Migration Reconciliation Runbook
+
+Use this runbook when working with the current file-to-SQLite migration surface.
+
+## Normal Flow
+
+1. Inspect scope
+   - `sce state plan --json`
+2. Diagnose drift
+   - `sce state doctor --json`
+3. Apply repair
+   - `sce state reconcile --all --apply --json`
+4. Re-check gate posture
+   - `node scripts/state-migration-reconciliation-gate.js --fail-on-blocking --fail-on-pending --json`
+
+## Severity Model
+
+### Blocking
+
+Treat these as release-blocking anomalies:
+
+- `sqlite-unavailable`
+- `source-parse-error`
+- `sqlite-ahead`
+- `sqlite-only`
+- runtime `sqlite-ahead`
+- runtime `sqlite-only`
+
+Typical meaning:
+
+- `sqlite-ahead`: SQLite contains index rows that are no longer represented by canonical files
+- `sqlite-only`: canonical file source disappeared but SQLite rows still exist
+
+### Alert
+
+Treat these as repairable but non-steady-state conditions:
+
+- `pending-migration`
+- `missing-source`
+- runtime `pending-sync`
+
+Typical meaning:
+
+- `pending-migration`: file source has more records than SQLite index
+- `missing-source`: the project does not currently have that source artifact
+
+## Operator Decisions
+
+### When `pending-migration`
+
+- Run `sce state reconcile --all --apply --json`
+- Re-run `sce state doctor --json`
+- If it persists, inspect source parser assumptions and source file health
+
+### When `sqlite-ahead`
+
+- Treat as anomaly first, not optimization
+- Inspect whether source artifacts were deleted, rotated, or never written
+- Rebuild or re-sync from canonical file source before release
+
+### When `sqlite-only`
+
+- Confirm whether the file source was removed accidentally
+- Restore canonical files when possible
+- Do not normalize this into a permanent state for current migration-scope components
+
+### When `missing-source`
+
+- If the component is intentionally unused in the current project, keep it advisory
+- If the component should exist for this workflow, generate or restore the source artifact and reconcile
+
+## Related Commands
+
+- `npm run gate:state-migration-reconciliation`
+- `npm run audit:state-storage`
+- `npm run report:interactive-approval-projection`

package/docs/state-storage-tiering.md

@@ -0,0 +1,104 @@
+# State Storage Tiering
+
+SCE uses a selective SQLite strategy.
+
+The operating rule is:
+
+- keep canonical evidence, audit, recovery payloads, and low-cardinality personal state in files
+- use SQLite for registry/index workloads with real query pressure
+- allow SQLite projections for append-only streams only when they are rebuildable from files
+
+## Tiers
+
+### `file-source`
+
+Use this tier when:
+
+- the file is the canonical evidence or audit artifact
+- the resource is a small personal or local configuration object
+- manual inspection, Git diff, and recovery are more important than indexed querying
+
+Examples:
+
+- `~/.sce/workspace-state.json`
+- `.sce/reports/**/*.jsonl`
+- `.sce/audit/**/*.jsonl`
+- `.sce/timeline/snapshots/**`
+- `.sce/session-governance/sessions/**`
+
+### `sqlite-index`
+
+Use this tier when:
+
+- the canonical content still lives in files
+- the resource behaves like a registry or index
+- repeated filtering, sorting, and cross-run queries justify an index
+
+Current active scope:
+
+- `collab.agent-registry` -> `.sce/config/agent-registry.json`
+- `runtime.timeline-index` -> `.sce/timeline/index.json`
+- `runtime.scene-session-index` -> `.sce/session-governance/scene-index.json`
+- `errorbook.entry-index` -> `.sce/errorbook/index.json`
+- `errorbook.incident-index` -> `.sce/errorbook/staging/index.json`
+- `governance.spec-scene-overrides` -> `.sce/spec-governance/spec-scene-overrides.json`
+- `governance.scene-index` -> `.sce/spec-governance/scene-index.json`
+- `release.evidence-runs-index` -> `.sce/reports/release-evidence/handoff-runs.json`
+- `release.gate-history-index` -> `.sce/reports/release-evidence/release-gate-history.json`
+
+### `derived-sqlite-projection`
+
+Use this tier only when:
+
+- the source remains append-only files
+- the projection can be deleted and rebuilt
+- reads clearly disclose when SQLite projection is used
+
+This tier is for query acceleration, not source-of-truth replacement.
+
+## Admission Rubric
+
+A resource should only enter SQLite scope when all of the following are true:
+
+1. Cross-run or cross-session query pressure is real.
+2. File scans are materially weaker than indexed filtering/sorting.
+3. SQLite rows are rebuildable from a canonical file or stream.
+4. Diagnostics, reconcile behavior, and operator guidance are defined up front.
+
+Reject SQLite source migration when any of the following are true:
+
+1. The resource is raw audit or evidence.
+2. The resource is low-cardinality workspace or preference state.
+3. Human-readable recovery and Git diff matter more than query speed.
+4. The change would silently cut over the source of truth.
+
+## Current Classification
+
+| Resource | Tier | Why |
+| --- | --- | --- |
+| `~/.sce/workspace-state.json` | `file-source` | Atomic personal state; no meaningful query pressure |
+| `.sce/reports/**/*.jsonl` | `file-source` | Canonical append-only governance/evidence streams |
+| `.sce/audit/**/*.jsonl` | `file-source` | Canonical audit evidence |
+| `.sce/timeline/index.json` | `sqlite-index` | Index-like query workload |
+| `.sce/session-governance/scene-index.json` | `sqlite-index` | Registry-like query workload |
+| `.sce/errorbook/index.json` | `sqlite-index` | Filtered status/quality lookup |
+| `.sce/errorbook/staging/index.json` | `sqlite-index` | Incident triage lookup |
+| `.sce/spec-governance/*.json` indexes | `sqlite-index` | Governance registry lookup |
+| `.sce/reports/release-evidence/handoff-runs.json` | `sqlite-index` | Historical release summary lookup |
+| `.sce/reports/release-evidence/release-gate-history.json` | `sqlite-index` | Gate history lookup |
+| `.sce/timeline/snapshots/**` | `file-source` | Recovery payloads |
+| `.sce/session-governance/sessions/**` | `file-source` | Session payload archives |
+
+## Operator Rules
+
+- Do not propose blanket sqlite-ization.
+- Before adding a new SQLite candidate, update `.sce/config/state-storage-policy.json`.
+- Run `npm run audit:state-storage` after changing state storage behavior.
+- If the resource is append-only evidence, prefer a projection pilot over source migration.
+
+## Related Assets
+
+- Policy file: `.sce/config/state-storage-policy.json`
+- Audit command: `npm run audit:state-storage`
+- Machine-readable report: `npm run report:state-storage`
+- State migration commands: `sce state plan|doctor|migrate|reconcile`

package/docs/zh/releases/README.md

@@ -9,6 +9,7 @@
 ## 历史版本归档
 
 - [发布检查清单](../release-checklist.md)
+- [v3.6.39 发布说明](./v3.6.39.md)
 - [v3.6.38 发布说明](./v3.6.38.md)
 - [v3.6.37 发布说明](./v3.6.37.md)
 - [v1.46.2 发布说明](./v1.46.2.md)（历史归档）

package/docs/zh/releases/v3.6.39.md

@@ -0,0 +1,24 @@
+# v3.6.39 发布说明
+
+发布日期：2026-03-13
+
+## 重点变化
+
+- 新增规范化的状态存储分层策略、迁移对账 runbook，以及配套 audit/report 工具，明确 SQLite 只承担受控索引层，不替代文件真源。
+- 扩展并加固了 `sce scene` 命令族，补齐多类命令覆盖、性质测试和 JSON summary 输出边界处理。
+- 完成 `115-00-sce-quality-hardening-program` 主 Spec 的集成收口，包含 `watch logs --follow` 补完，以及不依赖 `forceExit` 的 Jest open-handle 治理。
+
+## 验证
+
+- `node bin/sce.js collab status 115-00-sce-quality-hardening-program --graph`
+- `npm run test:smoke`
+- `npm run test:skip-audit`
+- `npm run test:brand-consistency`
+- `npm run test:full`
+- `npm run test:handles`
+
+## 发布说明
+
+- 状态持久化现在有了明确分层：证据、审计和操作员可读文件继续保持 canonical，SQLite 仅用于可重建索引或投影。
+- `scene` 命令面已经更接近稳定发布状态，publish/install/info/diff/validate/owner/tag/stats/lock/contribute/version 等流都有专门测试和 closeout 证据。
+- 质量门禁建议串行执行；`test:full` 与 `test:handles` 在串行场景下均已验证通过。

package/lib/commands/docs.js

@@ -301,6 +301,12 @@ async function handleConfigDisplay(configManager, reporter) {
     console.log(`  • ${dir}`);
   });
   console.log();
+
+  console.log(chalk.bold('Spec Allowed Root Files:'));
+  (config.specAllowedRootFiles || []).forEach(file => {
+    console.log(`  • ${file}`);
+  });
+  console.log();
   
   console.log(chalk.bold('Temporary Patterns:'));
   config.temporaryPatterns.forEach(pattern => {
@@ -350,10 +356,10 @@ async function handleConfigSet(configManager, reporter, options) {
   const camelKey = key.replace(/-([a-z])/g, (g) => g[1].toUpperCase());
   
   // Validate key
-  const validKeys = ['rootAllowedFiles', 'specSubdirs', 'temporaryPatterns'];
+  const validKeys = ['rootAllowedFiles', 'specAllowedRootFiles', 'specSubdirs', 'temporaryPatterns'];
   if (!validKeys.includes(camelKey)) {
     reporter.displayError(`Invalid configuration key: ${key}`);
-    console.log(chalk.gray('Valid keys: root-allowed-files, spec-subdirs, temporary-patterns\n'));
+    console.log(chalk.gray('Valid keys: root-allowed-files, spec-allowed-root-files, spec-subdirs, temporary-patterns\n'));
     return 2;
   }
   

package/lib/commands/scene.js

@@ -158,6 +158,45 @@ function createDoctorTraceId() {
   return `doctor-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
 }
 
+function stringifyJsonForCli(value, indentSize = 2, currentIndent = 0) {
+  if (value === null) {
+    return 'null';
+  }
+
+  if (typeof value === 'number') {
+    return Object.is(value, -0) ? '-0' : JSON.stringify(value);
+  }
+
+  if (typeof value === 'string' || typeof value === 'boolean') {
+    return JSON.stringify(value);
+  }
+
+  if (Array.isArray(value)) {
+    if (value.length === 0) {
+      return '[]';
+    }
+
+    const nextIndent = currentIndent + indentSize;
+    const indent = ' '.repeat(currentIndent);
+    const childIndent = ' '.repeat(nextIndent);
+    const items = value.map((entry) => `${childIndent}${stringifyJsonForCli(entry, indentSize, nextIndent)}`);
+    return `[\n${items.join(',\n')}\n${indent}]`;
+  }
+
+  const keys = Object.keys(value);
+  if (keys.length === 0) {
+    return '{}';
+  }
+
+  const nextIndent = currentIndent + indentSize;
+  const indent = ' '.repeat(currentIndent);
+  const childIndent = ' '.repeat(nextIndent);
+  const entries = keys.map((key) => (
+    `${childIndent}${JSON.stringify(key)}: ${stringifyJsonForCli(value[key], indentSize, nextIndent)}`
+  ));
+  return `{\n${entries.join(',\n')}\n${indent}}`;
+}
+
 function registerSceneCommands(program) {
   const sceneCmd = program
     .command('scene')
@@ -4795,7 +4834,7 @@ function createSceneEvalConfigTemplateByProfile(profile = 'default') {
 }
 
 function normalizeRelativePath(targetPath = '') {
-  return String(targetPath || '').replace(/\\/g, '/').replace(/\/+/g, '/').replace(/^\.\//, '');
+  return String(targetPath || '').trim().replace(/\\/g, '/').replace(/\/+/g, '/').replace(/^\.\//, '');
 }
 
 function collectManifestDiscoveryCandidates(preferredPath = 'custom/scene.yaml') {
@@ -13639,6 +13678,35 @@ async function runSceneVersionCommand(rawOptions = {}, dependencies = {}) {
   }
 }
 
+function isBinaryContent(buffer) {
+  if (!Buffer.isBuffer(buffer)) {
+    return false;
+  }
+
+  for (let index = 0; index < buffer.length; index++) {
+    if (buffer[index] === 0) {
+      return true;
+    }
+  }
+
+  return false;
+}
+
+function countChangedLines(fromContent, toContent) {
+  const oldLines = fromContent.toString('utf8').split('\n');
+  const newLines = toContent.toString('utf8').split('\n');
+  const maxLen = Math.max(oldLines.length, newLines.length);
+  let changedLines = 0;
+
+  for (let index = 0; index < maxLen; index++) {
+    if ((oldLines[index] || '') !== (newLines[index] || '')) {
+      changedLines++;
+    }
+  }
+
+  return changedLines;
+}
+
 function buildPackageDiff(fromFiles, toFiles) {
   const fromMap = new Map();
   for (const f of (fromFiles || [])) {
@@ -13662,19 +13730,9 @@ function buildPackageDiff(fromFiles, toFiles) {
       if (Buffer.compare(content, toContent) === 0) {
         unchanged.push(filePath);
       } else {
-        let changedLines = 0;
-        try {
-          const oldLines = content.toString('utf8').split('\n');
-          const newLines = toContent.toString('utf8').split('\n');
-          const maxLen = Math.max(oldLines.length, newLines.length);
-          for (let i = 0; i < maxLen; i++) {
-            if ((oldLines[i] || '') !== (newLines[i] || '')) {
-              changedLines++;
-            }
-          }
-        } catch (_e) {
-          changedLines = -1;
-        }
+        const changedLines = isBinaryContent(content) || isBinaryContent(toContent)
+          ? -1
+          : countChangedLines(content, toContent);
         modified.push({ path: filePath, changedLines });
       }
     }
@@ -13734,7 +13792,9 @@ function printSceneDiffSummary(options, payload, projectRoot = process.cwd()) {
       console.log(chalk.red(`  - ${f}`));
     }
     for (const f of payload.files.modified) {
-      const detail = f.changedLines >= 0 ? ` (${f.changedLines} lines changed)` : ' (binary content differs)';
+      const detail = options.stat
+        ? ''
+        : (f.changedLines >= 0 ? ` (${f.changedLines} lines changed)` : ' (binary content differs)');
       console.log(chalk.yellow(`  ~ ${f.path}${detail}`));
     }
   }
@@ -15248,7 +15308,7 @@ async function runSceneLintCommand(rawOptions = {}, dependencies = {}) {
 
 function printSceneLintSummary(options, payload, projectRoot = process.cwd()) {
   if (options.json) {
-    console.log(JSON.stringify(payload, null, 2));
+    console.log(stringifyJsonForCli(payload));
     return;
   }
 
@@ -15344,7 +15404,7 @@ async function runSceneScoreCommand(rawOptions = {}, dependencies = {}) {
 
 function printSceneScoreSummary(options, payload, projectRoot = process.cwd()) {
   if (options.json) {
-    console.log(JSON.stringify(payload, null, 2));
+    console.log(stringifyJsonForCli(payload));
     return;
   }
 
@@ -15524,7 +15584,7 @@ async function runSceneContributeCommand(rawOptions = {}, dependencies = {}) {
 
 function printSceneContributeSummary(options, payload, projectRoot = process.cwd()) {
   if (options.json) {
-    console.log(JSON.stringify(payload, null, 2));
+    console.log(stringifyJsonForCli(payload));
     return;
   }
 

package/lib/commands/watch.js

@@ -11,6 +11,15 @@ const inquirer = require('inquirer');
 const WatchManager = require('../watch/watch-manager');
 const { listPresets, getPreset, mergePreset, validatePreset } = require('../watch/presets');
 
+function sleep(ms) {
+  return new Promise(resolve => {
+    const timer = setTimeout(resolve, ms);
+    if (typeof timer.unref === 'function') {
+      timer.unref();
+    }
+  });
+}
+
 /**
  * Start watch mode
  * 
@@ -329,7 +338,7 @@ async function followLogStream(logPath, options = {}) {
         break;
       }
 
-      await new Promise(resolve => setTimeout(resolve, pollIntervalMs));
+      await sleep(pollIntervalMs);
     }
   } finally {
     process.removeListener('SIGINT', onSigInt);

package/lib/governance/config-manager.js

@@ -52,6 +52,12 @@ class ConfigManager {
         'CHANGELOG.md',
         'CONTRIBUTING.md'
       ],
+      specAllowedRootFiles: [
+        'requirements.md',
+        'design.md',
+        'tasks.md',
+        'collaboration.json'
+      ],
       specSubdirs: [
         'reports',
         'scripts',
@@ -152,6 +158,10 @@ class ConfigManager {
     if (!config.specSubdirs || !Array.isArray(config.specSubdirs)) {
       errors.push('specSubdirs must be an array');
     }
+
+    if (!config.specAllowedRootFiles || !Array.isArray(config.specAllowedRootFiles)) {
+      errors.push('specAllowedRootFiles must be an array');
+    }
     
     if (!config.temporaryPatterns || !Array.isArray(config.temporaryPatterns)) {
       errors.push('temporaryPatterns must be an array');
@@ -169,6 +179,12 @@ class ConfigManager {
         errors.push('specSubdirs must contain only strings');
       }
     }
+
+    if (config.specAllowedRootFiles && Array.isArray(config.specAllowedRootFiles)) {
+      if (config.specAllowedRootFiles.some(f => typeof f !== 'string')) {
+        errors.push('specAllowedRootFiles must contain only strings');
+      }
+    }
     
     if (config.temporaryPatterns && Array.isArray(config.temporaryPatterns)) {
       if (config.temporaryPatterns.some(p => typeof p !== 'string')) {

package/lib/governance/diagnostic-engine.js

@@ -81,6 +81,7 @@ class DiagnosticEngine {
   async scanSpecDirectory(specPath) {
     const specName = path.basename(specPath);
     const requiredFiles = ['requirements.md', 'design.md', 'tasks.md'];
+    const allowedRootFiles = this.config.specAllowedRootFiles || requiredFiles;
     
     // Check for missing required files
     for (const requiredFile of requiredFiles) {
@@ -124,7 +125,7 @@ class DiagnosticEngine {
       const basename = path.basename(filePath);
       
       // Skip required files
-      if (requiredFiles.includes(basename)) {
+      if (allowedRootFiles.includes(basename)) {
         continue;
       }