@ryuenn3123/agentic-senior-core 3.0.0 → 3.0.3

package/.agent-context/prompts/bootstrap-design.md

@@ -0,0 +1,22 @@
+
+# Bootstrap DESIGN.md (UI/UX Art Direction)
+
+When a user requests frontend design or redesign, the agent should automatically synthesize a complete DESIGN.md covering:
+- Visual identity (color palette, typography, spacing, iconography)
+- Layout and navigation principles
+- Component library and atomic design system
+- Accessibility and responsive guidelines
+- User journey and interaction flows
+- Design tokens and handoff notes for developers
+
+The agent must:
+1. Read [AGENTS.md](../../AGENTS.md) for project context and team roles.
+2. Scan all files in [.agent-context/rules/](../rules/) for UI/UX and accessibility standards.
+3. Reference [docs/deep-dive.md](../../docs/deep-dive.md) and [docs/faq.md](../../docs/faq.md) for architecture and product background.
+4. If [docs/DESIGN.md](../../docs/DESIGN.md) exists, check for drift and propose improvements instead of rewriting from scratch.
+5. All references to docs or rules must be clickable markdown links.
+
+Output:
+- Write a full DESIGN.md in markdown, with clear sections and clickable links to referenced docs/rules.
+- Use practical, modern, and accessible design language.
+- Wait for user approval before generating Figma or code assets.

package/.agent-context/prompts/init-project.md

@@ -1,7 +1,41 @@
-# Prompts: Initialize Project
 
-> Copy-paste one of these prompts to your AI agent (Cursor, Windsurf, Copilot, Antigravity) right after cloning this repository.
-> V1.4 recommendation: run `bunx @fatidaprilian/agentic-senior-core init` first to compile dynamic rules operations context (Federated Governance baseline).
+# Project Initialization Prompts
+
+This prompt boots a repository with strict rules operations context (Federated Governance baseline).
+
+When a new project is created or initialized, the agent should automatically:
+1. Read [AGENTS.md](../../AGENTS.md) to understand available roles and knowledge base.
+2. Scan all files in [.agent-context/rules/](../rules/) for mandatory engineering standards.
+3. Review dynamic stack and architecture signals from [docs/deep-dive.md](../../docs/deep-dive.md), [docs/faq.md](../../docs/faq.md), and task constraints.
+
+## Architect Mode (Recommended)
+If the user describes a project or feature, the agent should:
+1. Propose the most efficient technology stack based on requirements and evidence.
+2. Explain why this stack is the best choice for the project.
+3. Draft a high-level architecture plan.
+4. Wait for user approval before scaffolding the project using the selected architecture playbook.
+
+## Direct Blueprint Mode
+If the user specifies a framework/blueprint, the agent should:
+1. Read [AGENTS.md](../../AGENTS.md) for role context.
+2. Scan all files in [.agent-context/rules/](../rules/) for engineering standards.
+3. Reference [docs/deep-dive.md](../../docs/deep-dive.md) and [docs/faq.md](../../docs/faq.md) for stack/blueprint guidance.
+4. Scaffold the initial project structure following the blueprint exactly:
+	- Create all directories and files from the blueprint
+	- Set up environment config and validation (e.g., Zod, Pydantic, FluentValidation)
+	- Set up error handling foundation (base error class + global handler)
+	- Set up the logger
+	- Create a health check endpoint
+	- Initialize the ORM/Database connection
+	- Every file must follow [naming conventions](../rules/naming-conv.md)
+	- Every module must follow [architecture.md](../rules/architecture.md)
+	- Every dependency must be justified per [efficiency-vs-hype.md](../rules/efficiency-vs-hype.md)
+
+## Stacks & Blueprints Reference
+See [docs/roadmap.md](../../docs/roadmap.md) and [docs/deep-dive.md](../../docs/deep-dive.md) for the latest stack and blueprint list.
+
+## UI/UX Bootstrap
+When a user requests frontend or UI/UX design, the agent should automatically execute the [bootstrap-design.md](./bootstrap-design.md) prompt to synthesize DESIGN.md.
 
 ---
 
@@ -49,38 +83,20 @@ Now scaffold the initial project structure following the blueprint exactly:
 - Create a health check endpoint
 - Initialize the ORM/Database connection
 
-Every file MUST follow the naming conventions from rules/naming-conv.md.
-Every module MUST follow the architecture from rules/architecture.md.
-Every dependency MUST be justified per rules/efficiency-vs-hype.md.
+
+Every file must follow [naming conventions](../rules/naming-conv.md).
+Every module must follow [architecture.md](../rules/architecture.md).
+Every dependency must be justified per [efficiency-vs-hype.md](../rules/efficiency-vs-hype.md).
 ```
 
 ---
 
-## Available Stacks & Blueprints Reference
-
-### Stacks (`[STACK].md`)
-- `typescript`
-- `python`
-- `java`
-- `php`
-- `go`
-- `csharp`
-- `rust`
-- `ruby`
-
-### Blueprints (`[BLUEPRINT].md`)
-| Blueprint | Use When |
-|-----------|----------|
-| `api-nextjs` | Next.js App Router API project |
-| `nestjs-logic` | NestJS backend service |
-| `fastapi-service` | Python FastAPI backend service |
-| `laravel-api` | PHP Laravel 13 API |
-| `spring-boot-api`| Java Spring Boot 4 API |
-| `go-service` | Go chi HTTP service |
-| `aspnet-api` | C# ASP.NET Minimal API |
-| `ci-github-actions`| GitHub Actions CI/CD pipeline |
-| `ci-gitlab`      | GitLab CI/CD pipeline |
-| `observability`  | OpenTelemetry stack |
-| `graphql-grpc-api` | GraphQL / gRPC API definitions |
-| `infrastructure-as-code` | Infrastructure as Code (Terraform | Pulumi) |
-| `kubernetes-manifests` | Kubernetes manifests structure |
+## Stacks & Blueprints Reference
+
+See [docs/roadmap.md](../../docs/roadmap.md) and [docs/deep-dive.md](../../docs/deep-dive.md) for the latest stack and blueprint list.
+
+---
+
+## Bootstrap UI/UX (DESIGN.md)
+
+To start UI/UX design from scratch, use the [bootstrap-design.md](./bootstrap-design.md) prompt to synthesize `docs/DESIGN.md`.

package/.agent-context/state/memory-continuity-benchmark.json

@@ -1,5 +1,5 @@
 {
-  "generatedAt": "2026-04-18T12:31:23.643Z",
+  "generatedAt": "2026-04-18T13:26:49.303Z",
   "reportName": "memory-continuity-benchmark",
   "schemaVersion": "1.0.0",
   "passed": true,

package/.cursorrules

@@ -1,6 +1,6 @@
 # AGENTIC-SENIOR-CORE DYNAMIC GOVERNANCE RULESET
 
-Generated by Agentic-Senior-Core CLI v3.0.0
+Generated by Agentic-Senior-Core CLI v3.0.3
 Timestamp: 2026-04-18T00:00:00.000Z
 Selected profile: beginner
 Selected policy file: .agent-context/policies/llm-judge-threshold.json

package/.windsurfrules

@@ -1,6 +1,6 @@
 # AGENTIC-SENIOR-CORE DYNAMIC GOVERNANCE RULESET
 
-Generated by Agentic-Senior-Core CLI v3.0.0
+Generated by Agentic-Senior-Core CLI v3.0.3
 Timestamp: 2026-04-18T00:00:00.000Z
 Selected profile: beginner
 Selected policy file: .agent-context/policies/llm-judge-threshold.json

package/README.md

@@ -10,7 +10,7 @@
 **Production-grade Rules Engine (Governance Engine) for AI coding agents.**
 Works with Cursor, Windsurf, GitHub Copilot, Claude Code, Gemini, and other LLM-powered IDE workflows.
 
-Latest release: 3.0.0 (2026-04-18).
+Latest release: 3.0.3 (2026-04-18).
 
 Highlights in 3.0.0:
 - Universal IDE adapter surface is completed and synchronized through thin adapters.
@@ -21,63 +21,17 @@ Highlights in 3.0.0:
 
 ---
 
-## 60-Second Start
-
-```bash
-npx @ryuenn3123/agentic-senior-core init
-```
-
-That one command initializes your project with compiled rules, review checklists, and state context.
-
-Golden Standard mode is now the default path: init applies the recommended quality profile automatically, without a beginner/balanced/strict prompt on first run.
-
-Optional team default path:
-
-```bash
-npx @ryuenn3123/agentic-senior-core init --profile-pack startup
-```
-
-Project-description-first path (AI as Architect with veto control):
-
-```bash
-npx @ryuenn3123/agentic-senior-core init --project-description "Machine learning API for fraud detection"
-```
-
-Default init path now attempts trusted realtime stack research first (with automatic snapshot fallback):
 
-```bash
-npx @ryuenn3123/agentic-senior-core init --project-description "Event-driven payments platform"
-```
-
-Force deterministic snapshot-only mode:
-
-```bash
-npx @ryuenn3123/agentic-senior-core init --project-description "Event-driven payments platform" --architect-research-mode snapshot
-```
+## 60-Second Start
 
-Optional trusted realtime enrichment (explicitly gated):
 
 ```bash
-npx @ryuenn3123/agentic-senior-core init --project-description "Modern conversion-focused product website" --architect-research-mode realtime --enable-realtime-research --architect-realtime-signal-file ./realtime-signals.json
+npx @ryuenn3123/agentic-senior-core init
 ```
 
-AI-first project context bootstrap (no static docs template rendering):
+One command to initialize rules, checklists, and strict AI coding guidelines context for your project.
 
-- Init now generates bootstrap prompts under `.agent-context/prompts/`.
-- On first IDE chat, execute `bootstrap-project-context.md` when `docs/project-brief.md` is missing.
-- For UI-first projects, execute `bootstrap-design.md` when `docs/DESIGN.md` is missing.
-- The assistant should synthesize docs from scratch into `docs/` and treat them as living context.
-
-Canonical instruction output (multi-tool bridge):
-
-- Init now generates `.agent-instructions.md` as canonical instruction source.
-- Init also syncs adapter files for tool compatibility: `.cursorrules`, `.windsurfrules`, `.clauderc`, `.gemini/instructions.md`, and `.github/copilot-instructions.md`.
-
-V3 purge readiness dry-run (no deletion):
-
-```bash
-npm run audit:v3-purge
-```
+> **See [docs/deep-dive.md](docs/deep-dive.md) and [docs/roadmap.md](docs/roadmap.md) for advanced configuration, architect mode, snapshot, and realtime options.**
 
 - This command writes `.agent-context/state/v3-purge-audit.json` and reports whether static directory deletion is safe.
 
@@ -119,7 +73,7 @@ If you see `Property $schema is not allowed`, keep `.vscode/mcp.json` without `$
 
 | Command | Purpose |
 |---------|---------|
-| `agentic-senior-core init` | Initialize rules operations context (Federated Governance baseline) |
+| `agentic-senior-core init` | Initialize strict AI coding guidelines (Federated Governance baseline) |
 | `agentic-senior-core upgrade --dry-run` | Preview safe upgrades |
 | `agentic-senior-core optimize --show` | Show token optimization state |
 | `npm run audit:v3-purge` | Run deep purge readiness audit (no deletion) |
@@ -136,6 +90,9 @@ npx @ryuenn3123/agentic-senior-core upgrade --yes
 
 Use `--dry-run` first to preview changes safely, then apply with `--yes`.
 
+Upgrade now performs managed-surface synchronization by default: obsolete governance files under managed paths are pruned so the pack stays aligned with the latest release.
+Use `--no-prune` if you want to keep legacy managed files.
+
 ---
 
 ## Terminology Mapping (Final)

package/lib/cli/commands/upgrade.mjs

@@ -21,6 +21,7 @@ import {
   collectFileNames,
   formatDuration,
   pathExists,
+  analyzeManagedGovernanceSurface,
   copyGovernanceAssetsToTarget,
 } from '../utils.mjs';
 
@@ -46,7 +47,8 @@ export function parseUpgradeArguments(commandArguments) {
     targetDirectory: '.',
     dryRun: false,
     skipConfirmation: false,
-    includeMcpTemplate: false,
+    includeMcpTemplate: true,
+    pruneManagedSurface: true,
   };
 
   for (let argumentIndex = 0; argumentIndex < commandArguments.length; argumentIndex++) {
@@ -72,6 +74,21 @@ export function parseUpgradeArguments(commandArguments) {
       continue;
     }
 
+    if (currentArgument === '--no-mcp-template') {
+      parsedUpgradeOptions.includeMcpTemplate = false;
+      continue;
+    }
+
+    if (currentArgument === '--prune') {
+      parsedUpgradeOptions.pruneManagedSurface = true;
+      continue;
+    }
+
+    if (currentArgument === '--no-prune') {
+      parsedUpgradeOptions.pruneManagedSurface = false;
+      continue;
+    }
+
     throw new Error(`Unknown option: ${currentArgument}`);
   }
 
@@ -112,9 +129,7 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
     console.log(`\nAgentic-Senior-Core CLI v${CLI_VERSION}`);
     console.log('Running rules operations upgrade assistant (Federated Governance baseline) for an existing repository.');
 
-    await copyGovernanceAssetsToTarget(resolvedTargetDirectoryPath, {
-      includeMcpTemplate: upgradeOptions.includeMcpTemplate === true,
-    });
+    const managedSurfacePlan = await analyzeManagedGovernanceSurface(resolvedTargetDirectoryPath);
 
     const stackFileNames = await collectFileNames(path.join(AGENT_CONTEXT_DIR, 'stacks'));
     const blueprintFileNames = await collectFileNames(path.join(AGENT_CONTEXT_DIR, 'blueprints'));
@@ -239,12 +254,30 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
     console.log(`- Existing rules lines: ${currentRuleLineCount}`);
     console.log(`- Planned rules lines: ${plannedRuleLineCount}`);
     console.log(`- Rules changed: ${isRulesContentChanged ? 'yes' : 'no'}`);
+    console.log(`- Managed surface stale files: ${managedSurfacePlan.staleFiles.length}`);
+    console.log(`- Managed surface stale directories: ${managedSurfacePlan.staleDirectories.length}`);
+    console.log(`- Managed surface prune mode: ${upgradeOptions.pruneManagedSurface === true ? 'enabled (default)' : 'disabled (--no-prune)'}`);
+    console.log(`- MCP config write mode: ${upgradeOptions.includeMcpTemplate === true ? 'enabled (default)' : 'disabled (--no-mcp-template)'}`);
     if (projectDocStalenessReport.hasProjectDocs) {
       console.log(`- Project docs detected: ${projectDocStalenessReport.checkedFileNames.length}`);
       console.log(`- Project docs expected template version: ${projectDocStalenessReport.expectedTemplateVersion}`);
       console.log(`- Project docs stale files: ${projectDocStalenessReport.staleFiles.length}`);
     }
 
+    if (managedSurfacePlan.staleFiles.length > 0 || managedSurfacePlan.staleDirectories.length > 0) {
+      console.log('\nManaged surface stale paths preview (up to 5):');
+      const previewPaths = [
+        ...managedSurfacePlan.staleFiles,
+        ...managedSurfacePlan.staleDirectories,
+      ].slice(0, 5);
+      for (const previewPath of previewPaths) {
+        console.log(`- ${previewPath}`);
+      }
+      if (managedSurfacePlan.staleFiles.length + managedSurfacePlan.staleDirectories.length > previewPaths.length) {
+        console.log('- ...');
+      }
+    }
+
     if (projectDocStalenessReport.staleFiles.length > 0) {
       console.log('\n[WARN] Some project docs were generated from older template versions:');
       for (const staleDoc of projectDocStalenessReport.staleFiles) {
@@ -261,7 +294,7 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
 
     const shouldApplyUpgrade = upgradeOptions.skipConfirmation
       ? true
-      : await askYesNo('Apply upgrade and write migrated files?', userInterface, true);
+      : await askYesNo('Apply upgrade and synchronize managed files?', userInterface, true);
 
     if (!shouldApplyUpgrade) {
       console.log('Upgrade cancelled by user.');
@@ -271,6 +304,12 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
     await createBackup(resolvedTargetDirectoryPath);
 
     try {
+      const governanceSyncResult = await copyGovernanceAssetsToTarget(resolvedTargetDirectoryPath, {
+        includeMcpTemplate: upgradeOptions.includeMcpTemplate === true,
+        pruneManagedSurface: upgradeOptions.pruneManagedSurface === true,
+        managedSurfacePlan,
+      });
+
       await fs.writeFile(currentRulesPath, plannedRulesContent, 'utf8');
       await fs.writeFile(path.join(resolvedTargetDirectoryPath, '.windsurfrules'), plannedRulesContent, 'utf8');
       await writeSelectedPolicy(resolvedTargetDirectoryPath, selectedProfileName);
@@ -294,6 +333,8 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
 
       console.log('\nUpgrade complete.');
       console.log(`- Rules rewritten: ${isRulesContentChanged ? 'yes' : 'no (metadata refreshed)'}`);
+      console.log(`- Managed stale files removed: ${governanceSyncResult.deletedManagedFiles.length}`);
+      console.log(`- Managed stale directories removed: ${governanceSyncResult.deletedManagedDirectories.length}`);
       console.log(`- Setup time: ${formatDuration(setupDurationMs)}`);
       console.log('- Updated files: .cursorrules, .windsurfrules, .agent-context/state/onboarding-report.json');
     } catch (error) {

package/lib/cli/utils.mjs

@@ -29,7 +29,7 @@ export function printUsage() {
   console.log('Usage:');
   console.log('  agentic-senior-core launch');
   console.log('  agentic-senior-core init [target-directory] [--preset <name>] [--profile <beginner|balanced|strict>] [--profile-pack <name>] [--stack <name>] [--blueprint <name>] [--project-description <text>] [--architect-token-budget <number>] [--architect-timeout-ms <number>] [--architect-research-mode <snapshot|realtime>] [--enable-realtime-research] [--architect-realtime-signal-file <path>] [--ci <true|false>] [--newbie] [--token-optimize] [--no-token-optimize] [--token-agent <name>] [--memory-continuity] [--no-memory-continuity] [--scaffold-docs] [--no-scaffold-docs] [--docs-lang <en|id>] [--project-config <path>] [--runtime-env <auto|linux-wsl|linux|windows|macos>]');
-  console.log('  agentic-senior-core upgrade [target-directory] [--dry-run] [--yes] [--mcp-template]');
+  console.log('  agentic-senior-core upgrade [target-directory] [--dry-run] [--yes] [--mcp-template] [--no-mcp-template] [--prune] [--no-prune]');
   console.log('  agentic-senior-core optimize [target-directory] [--agent <copilot|claude|cursor|windsurf|gemini|codex|cline>] [--enable|--disable] [--show]');
   console.log('  agentic-senior-core mcp');
   console.log('  agentic-senior-core rollback [target-directory]');
@@ -66,6 +66,8 @@ export function printUsage() {
   console.log('  --runtime-env   Override runtime environment hint (auto, linux-wsl, linux, windows, macos)');
   console.log('  --dry-run    Preview upgrade without writing files');
   console.log('  --yes        Skip confirmation prompts for upgrade');
+  console.log('  --prune      Keep managed governance files synchronized 1:1 (default in upgrade)');
+  console.log('  --no-prune   Do not remove stale managed governance files during upgrade');
   console.log('  --agent      Target agent integration for token optimization mode');
   console.log('  --enable     Enable token optimization policy and rebuild compiled rules');
   console.log('  --disable    Disable token optimization policy and rebuild compiled rules');
@@ -110,11 +112,188 @@ export async function copyDirectory(sourceDirectoryPath, targetDirectoryPath) {
   }
 }
 
+function toPosixRelativePath(relativePath) {
+  return relativePath.split(path.sep).join('/');
+}
+
+function isPathWithinPrefix(relativePath, prefixPath) {
+  const normalizedRelativePath = toPosixRelativePath(relativePath).replace(/\/+$/g, '');
+  const normalizedPrefixPath = toPosixRelativePath(prefixPath).replace(/\/+$/g, '');
+
+  if (!normalizedPrefixPath) {
+    return false;
+  }
+
+  return normalizedRelativePath === normalizedPrefixPath
+    || normalizedRelativePath.startsWith(`${normalizedPrefixPath}/`);
+}
+
+async function collectRelativeTreeEntries(baseDirectoryPath, relativeRootPath) {
+  const files = [];
+  const directories = [];
+
+  if (!(await pathExists(baseDirectoryPath))) {
+    return { files, directories };
+  }
+
+  const normalizedRootPath = toPosixRelativePath(relativeRootPath);
+  directories.push(normalizedRootPath);
+
+  async function walkDirectory(currentDirectoryPath, currentRelativePath) {
+    const directoryEntries = await fs.readdir(currentDirectoryPath, { withFileTypes: true });
+
+    for (const directoryEntry of directoryEntries) {
+      const sourceEntryPath = path.join(currentDirectoryPath, directoryEntry.name);
+      const relativeEntryPath = toPosixRelativePath(path.join(currentRelativePath, directoryEntry.name));
+
+      if (directoryEntry.isDirectory()) {
+        directories.push(relativeEntryPath);
+        await walkDirectory(sourceEntryPath, relativeEntryPath);
+        continue;
+      }
+
+      files.push(relativeEntryPath);
+    }
+  }
+
+  await walkDirectory(baseDirectoryPath, normalizedRootPath);
+  return { files, directories };
+}
+
+async function buildManagedSourceManifest() {
+  const sourceFiles = new Set();
+  const sourceDirectories = new Set();
+
+  for (const sourceDirectoryName of directoryCopies) {
+    const sourceDirectoryPath = path.join(REPO_ROOT, sourceDirectoryName);
+    const sourceTreeEntries = await collectRelativeTreeEntries(sourceDirectoryPath, sourceDirectoryName);
+
+    for (const sourceFilePath of sourceTreeEntries.files) {
+      sourceFiles.add(sourceFilePath);
+    }
+
+    for (const sourceDirectoryPathRelative of sourceTreeEntries.directories) {
+      sourceDirectories.add(sourceDirectoryPathRelative);
+    }
+  }
+
+  for (const entryPointFileName of entryPointFiles) {
+    const sourceFilePath = path.join(REPO_ROOT, entryPointFileName);
+    if (!(await pathExists(sourceFilePath))) {
+      continue;
+    }
+
+    sourceFiles.add(toPosixRelativePath(entryPointFileName));
+  }
+
+  return {
+    files: sourceFiles,
+    directories: sourceDirectories,
+  };
+}
+
+async function collectManagedTargetManifest(resolvedTargetDirectoryPath) {
+  const targetFiles = new Set();
+  const targetDirectories = new Set();
+
+  for (const sourceDirectoryName of directoryCopies) {
+    const targetDirectoryPath = path.join(resolvedTargetDirectoryPath, sourceDirectoryName);
+    const targetTreeEntries = await collectRelativeTreeEntries(targetDirectoryPath, sourceDirectoryName);
+
+    for (const targetFilePath of targetTreeEntries.files) {
+      targetFiles.add(targetFilePath);
+    }
+
+    for (const targetDirectoryPathRelative of targetTreeEntries.directories) {
+      targetDirectories.add(targetDirectoryPathRelative);
+    }
+  }
+
+  for (const entryPointFileName of entryPointFiles) {
+    const targetFilePath = path.join(resolvedTargetDirectoryPath, entryPointFileName);
+    if (!(await pathExists(targetFilePath))) {
+      continue;
+    }
+
+    targetFiles.add(toPosixRelativePath(entryPointFileName));
+  }
+
+  return {
+    files: targetFiles,
+    directories: targetDirectories,
+  };
+}
+
+export async function analyzeManagedGovernanceSurface(
+  resolvedTargetDirectoryPath,
+  options = {}
+) {
+  const preservePathPrefixes = Array.isArray(options.preservePathPrefixes)
+    ? options.preservePathPrefixes
+    : ['.agent-context/state'];
+
+  const sourceManifest = await buildManagedSourceManifest();
+  const targetManifest = await collectManagedTargetManifest(resolvedTargetDirectoryPath);
+
+  const staleFiles = [];
+  const staleDirectories = [];
+  const preservedFiles = [];
+  const preservedDirectories = [];
+
+  const sortedTargetFiles = [...targetManifest.files].sort((leftPath, rightPath) => leftPath.localeCompare(rightPath));
+  const sortedTargetDirectories = [...targetManifest.directories].sort(
+    (leftPath, rightPath) => rightPath.length - leftPath.length || leftPath.localeCompare(rightPath)
+  );
+
+  for (const targetFilePath of sortedTargetFiles) {
+    if (sourceManifest.files.has(targetFilePath)) {
+      continue;
+    }
+
+    if (preservePathPrefixes.some((prefixPath) => isPathWithinPrefix(targetFilePath, prefixPath))) {
+      preservedFiles.push(targetFilePath);
+      continue;
+    }
+
+    staleFiles.push(targetFilePath);
+  }
+
+  for (const targetDirectoryPathRelative of sortedTargetDirectories) {
+    if (sourceManifest.directories.has(targetDirectoryPathRelative)) {
+      continue;
+    }
+
+    if (preservePathPrefixes.some((prefixPath) => isPathWithinPrefix(targetDirectoryPathRelative, prefixPath))) {
+      preservedDirectories.push(targetDirectoryPathRelative);
+      continue;
+    }
+
+    staleDirectories.push(targetDirectoryPathRelative);
+  }
+
+  return {
+    staleFiles,
+    staleDirectories,
+    preservedFiles,
+    preservedDirectories,
+    managedSourceFileCount: sourceManifest.files.size,
+    managedSourceDirectoryCount: sourceManifest.directories.size,
+    managedTargetFileCount: targetManifest.files.size,
+    managedTargetDirectoryCount: targetManifest.directories.size,
+  };
+}
+
 export async function copyGovernanceAssetsToTarget(
   resolvedTargetDirectoryPath,
   options = {}
 ) {
   const shouldIncludeMcpTemplate = options.includeMcpTemplate === true;
+  const shouldPruneManagedSurface = options.pruneManagedSurface === true;
+  const managedSurfacePlan = shouldPruneManagedSurface
+    ? options.managedSurfacePlan || await analyzeManagedGovernanceSurface(resolvedTargetDirectoryPath)
+    : null;
+  const deletedManagedFiles = [];
+  const deletedManagedDirectories = [];
 
   for (const sourceDirectoryName of directoryCopies) {
     const sourceDirectoryPath = path.join(REPO_ROOT, sourceDirectoryName);
@@ -141,6 +320,28 @@ export async function copyGovernanceAssetsToTarget(
     await fs.copyFile(sourceFilePath, targetFilePath);
   }
 
+  if (shouldPruneManagedSurface && managedSurfacePlan) {
+    for (const staleFileRelativePath of managedSurfacePlan.staleFiles) {
+      const staleFilePath = path.join(resolvedTargetDirectoryPath, ...staleFileRelativePath.split('/'));
+      if (!(await pathExists(staleFilePath))) {
+        continue;
+      }
+
+      await fs.unlink(staleFilePath);
+      deletedManagedFiles.push(staleFileRelativePath);
+    }
+
+    for (const staleDirectoryRelativePath of managedSurfacePlan.staleDirectories) {
+      const staleDirectoryPath = path.join(resolvedTargetDirectoryPath, ...staleDirectoryRelativePath.split('/'));
+      if (!(await pathExists(staleDirectoryPath))) {
+        continue;
+      }
+
+      await fs.rm(staleDirectoryPath, { recursive: true, force: true });
+      deletedManagedDirectories.push(staleDirectoryRelativePath);
+    }
+  }
+
   if (shouldIncludeMcpTemplate) {
     const projectName = path.basename(resolvedTargetDirectoryPath);
     const mcpArgs = ['./scripts/mcp-server.mjs'];
@@ -235,6 +436,12 @@ export async function copyGovernanceAssetsToTarget(
     }
   }
 
+  return {
+    deletedManagedFiles,
+    deletedManagedDirectories,
+    managedSurfacePlan,
+  };
+
 }
 
 export async function askChoice(promptMessage, options, userInterface) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ryuenn3123/agentic-senior-core",
-  "version": "3.0.0",
+  "version": "3.0.3",
   "type": "module",
   "description": "Force your AI Agent to code like a Staff Engineer, not a Junior.",
   "bin": {