@ryuenn3123/agentic-senior-core 3.0.47 → 3.0.48

package/lib/cli/commands/optimize.mjs

@@ -2,11 +2,7 @@ import fs from 'node:fs/promises';
 import path from 'node:path';
 
 import { ensureDirectory, formatDuration } from '../utils.mjs';
-import { compileDynamicContext, loadOnboardingReportIfExists } from '../compiler.mjs';
-import {
-  AGENT_DECISION_STACK_FILE_NAME,
-  AGENT_DECISION_BLUEPRINT_FILE_NAME,
-} from '../constants.mjs';
+import { loadOnboardingReportIfExists } from '../compiler.mjs';
 import {
   TOKEN_OPTIMIZATION_REPORT_FILE_NAME,
   normalizeAgentName,
@@ -18,17 +14,6 @@ import {
   writeTokenOptimizationState,
 } from '../token-optimization.mjs';
 
-function normalizeMarkdownFileName(rawFileName, fallbackFileName) {
-  if (typeof rawFileName !== 'string' || rawFileName.trim().length === 0) {
-    return fallbackFileName;
-  }
-
-  const normalizedFileName = rawFileName.trim();
-  return normalizedFileName.endsWith('.md')
-    ? normalizedFileName
-    : `${normalizedFileName}.md`;
-}
-
 export function parseOptimizeArguments(commandArguments) {
   const parsedOptimizeOptions = {
     targetDirectory: '.',
@@ -119,37 +104,6 @@ export async function runOptimizeCommand(targetDirectoryArgument, optimizeOption
 
   await writeTokenOptimizationState(resolvedTargetDirectoryPath, tokenOptimizationState);
 
-  const hasExplicitRuntimeConstraint = onboardingReport?.runtimeDecision?.mode === 'explicit-constraint';
-  const hasExplicitArchitectureConstraint = onboardingReport?.architectureDecision?.mode === 'explicit-constraint';
-  const selectedStackFileName = hasExplicitRuntimeConstraint
-    ? normalizeMarkdownFileName(onboardingReport.selectedStack, AGENT_DECISION_STACK_FILE_NAME)
-    : AGENT_DECISION_STACK_FILE_NAME;
-  const selectedAdditionalStackFileNames = hasExplicitRuntimeConstraint && Array.isArray(onboardingReport.selectedAdditionalStacks)
-    ? onboardingReport.selectedAdditionalStacks
-      .map((stackFileName) => normalizeMarkdownFileName(stackFileName, ''))
-      .filter((stackFileName) => stackFileName && stackFileName !== selectedStackFileName)
-    : [];
-  const selectedBlueprintFileName = hasExplicitArchitectureConstraint
-    ? normalizeMarkdownFileName(onboardingReport.selectedBlueprint, AGENT_DECISION_BLUEPRINT_FILE_NAME)
-    : AGENT_DECISION_BLUEPRINT_FILE_NAME;
-  const selectedAdditionalBlueprintFileNames = hasExplicitArchitectureConstraint && Array.isArray(onboardingReport.selectedAdditionalBlueprints)
-    ? onboardingReport.selectedAdditionalBlueprints
-      .map((blueprintFileName) => normalizeMarkdownFileName(blueprintFileName, ''))
-      .filter((blueprintFileName) => blueprintFileName && blueprintFileName !== selectedBlueprintFileName)
-    : [];
-  const includeCiGuardrails = typeof onboardingReport.ciGuardrailsEnabled === 'boolean'
-    ? onboardingReport.ciGuardrailsEnabled
-    : true;
-
-  await compileDynamicContext({
-    targetDirectoryPath: resolvedTargetDirectoryPath,
-    selectedStackFileName,
-    selectedAdditionalStackFileNames,
-    selectedBlueprintFileName,
-    selectedAdditionalBlueprintFileNames,
-    includeCiGuardrails,
-  });
-
   const optimizationDurationMs = Date.now() - optimizationStartedAt;
   const tokenOptimizationReport = {
     generatedAt: new Date().toISOString(),
@@ -174,7 +128,7 @@ export async function runOptimizeCommand(targetDirectoryArgument, optimizeOption
   console.log(`- Agent profile: ${tokenOptimizationState.selectedAgent}`);
   console.log(`- Preferred shell proxy: ${tokenOptimizationState.preferredShellProxy}`);
   console.log(`- Setup time: ${formatDuration(optimizationDurationMs)}`);
-  console.log('- Updated files: .agent-instructions.md, legacy thin adapters, and .agent-context/state/token-optimization.json');
+  console.log('- Updated files: .agent-context/state/token-optimization.json and .agent-context/state/token-optimization-report.json');
 
   if (tokenOptimizationState.enabled) {
     if (rtkDetection.isAvailable) {

package/lib/cli/commands/upgrade.mjs

@@ -33,8 +33,6 @@ import {
   detectUiScopeSignals,
 } from '../detector.mjs';
 import {
-  buildCompiledRulesContent,
-  compileDynamicContext,
   writeSelectedPolicy,
   writeOnboardingReport,
   loadOnboardingReportIfExists,
@@ -55,7 +53,7 @@ export function parseUpgradeArguments(commandArguments) {
     targetDirectory: '.',
     dryRun: false,
     skipConfirmation: false,
-    includeMcpTemplate: true,
+    includeMcpTemplate: false,
     pruneManagedSurface: true,
   };
 
@@ -243,19 +241,10 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
       declarationShown: true,
       detectionSummary: buildDetectionSummary(projectDetection),
       activeRulesSummary: {
-        canonicalSource: '.instructions.md',
-        compiledRulebook: '.agent-instructions.md',
-        legacyThinAdapters: ['.cursorrules', '.windsurfrules', '.clauderc'],
-        generatedBridgeAdapters: [
-          'AGENTS.md',
-          'CLAUDE.md',
-          'GEMINI.md',
-          '.cursor/rules/agentic-senior-core.mdc',
-          '.windsurf/rules/agentic-senior-core.md',
-          '.github/copilot-instructions.md',
-          '.github/instructions/agentic-senior-core.instructions.md',
-          '.gemini/instructions.md',
-        ],
+        canonicalSource: 'AGENTS.md',
+        compiledRulebook: null,
+        legacyThinAdapters: [],
+        generatedBridgeAdapters: ['CLAUDE.md', 'GEMINI.md'],
         stackLoadingMode: 'lazy',
         domainRuleLoadingMode: 'lazy',
         selectedProfile: selectedProfileName,
@@ -285,7 +274,7 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
     } else {
       console.log('- Detected stack: unresolved (insufficient markers).');
     }
-    console.log('- Active rules baseline: canonical .instructions.md -> compiled .agent-instructions.md + legacy thin root adapters');
+    console.log('- Active rules baseline: canonical AGENTS.md + .agent-context/ lazy rule library');
     console.log(
       `- Active review thresholds: ${(
         PROFILE_PRESETS[selectedProfileName]?.blockingSeverities || []
@@ -300,24 +289,6 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
 
     const projectDocStalenessReport = await detectProjectDocTemplateStaleness(resolvedTargetDirectoryPath);
 
-    const currentRulesPath = path.join(resolvedTargetDirectoryPath, '.agent-instructions.md');
-    const currentRulesContent = await pathExists(currentRulesPath)
-      ? await fs.readFile(currentRulesPath, 'utf8')
-      : '';
-
-    const plannedRulesContent = await buildCompiledRulesContent({
-      targetDirectoryPath: resolvedTargetDirectoryPath,
-      selectedStackFileName,
-      selectedAdditionalStackFileNames,
-      selectedBlueprintFileName,
-      selectedAdditionalBlueprintFileNames,
-      includeCiGuardrails,
-    });
-
-    const isRulesContentChanged = currentRulesContent !== plannedRulesContent;
-    const currentRuleLineCount = currentRulesContent ? currentRulesContent.split(/\r?\n/).length : 0;
-    const plannedRuleLineCount = plannedRulesContent.split(/\r?\n/).length;
-
     console.log('\nUpgrade preview:');
     console.log(`- Target directory: ${resolvedTargetDirectoryPath}`);
     console.log(`- Runtime decision: ${selectedStackFileName === AGENT_DECISION_STACK_FILE_NAME ? 'agent recommendation required from repo evidence' : toTitleCase(selectedStackFileName)}`);
@@ -329,14 +300,12 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
       console.log(`- Additional blueprints: ${selectedAdditionalBlueprintFileNames.map((blueprintFileName) => toTitleCase(blueprintFileName)).join(', ')}`);
     }
     console.log(`- CI/CD quality checks (guardrails): ${includeCiGuardrails ? 'enabled' : 'disabled'}`);
-    console.log(`- Existing rules lines: ${currentRuleLineCount}`);
-    console.log(`- Planned rules lines: ${plannedRuleLineCount}`);
-    console.log(`- Rules changed: ${isRulesContentChanged ? 'yes' : 'no'}`);
+    console.log('- Instruction surface: AGENTS.md canonical with CLAUDE.md and GEMINI.md import bridges');
     console.log(`- Managed surface stale files: ${managedSurfacePlan.staleFiles.length}`);
     console.log(`- Managed surface stale directories: ${managedSurfacePlan.staleDirectories.length}`);
     console.log(`- Managed surface sync mode: 1:1 (prune enabled)`);
     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)'}`);
+    console.log(`- MCP config write mode: ${upgradeOptions.includeMcpTemplate === true ? 'enabled (--mcp-template)' : 'disabled (default)'}`);
     if (projectDocStalenessReport.hasProjectDocs) {
       console.log(`- Project docs detected: ${projectDocStalenessReport.checkedFileNames.length}`);
       console.log(`- Project docs expected template version: ${projectDocStalenessReport.expectedTemplateVersion}`);
@@ -431,15 +400,6 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
         }
       }
 
-      const compileResult = await compileDynamicContext({
-        targetDirectoryPath: resolvedTargetDirectoryPath,
-        selectedStackFileName,
-        selectedAdditionalStackFileNames,
-        selectedBlueprintFileName,
-        selectedAdditionalBlueprintFileNames,
-        includeCiGuardrails,
-        preserveUserOwnedEntrypoints: true,
-      });
       await writeSelectedPolicy(resolvedTargetDirectoryPath, selectedProfileName);
 
       const setupDurationMs = Date.now() - setupStartedAt;
@@ -462,10 +422,8 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
 
       console.log('\nUpgrade complete.');
       console.log(`- Governance surface sync: 1:1 (${governanceSyncResult.updatedFiles.length} updated, ${governanceSyncResult.createdFiles.length} new, ${governanceSyncResult.deletedManagedFiles.length} deleted, ${governanceSyncResult.unchangedFiles.length} unchanged)`);
-      console.log(`- Rules rewritten: ${isRulesContentChanged ? 'yes' : 'no (metadata refreshed)'}`);
       const preservedInstructionEntrypoints = Array.from(new Set([
         ...(governanceSyncResult.preservedFiles || []),
-        ...(compileResult.preservedEntrypoints || []),
       ])).sort();
       if (preservedInstructionEntrypoints.length > 0) {
         console.log(`- User-owned instruction entrypoints preserved: ${preservedInstructionEntrypoints.length}`);
@@ -494,7 +452,7 @@ export async function runUpgradeCommand(targetDirectoryArgument, upgradeOptions
         supplementalCreatedFileNames.forEach((fileName) => console.log(`  [NEW]     ${fileName} (seed)`));
       }
 
-      console.log('\nRefreshed files: .instructions.md, .agent-instructions.md, legacy thin adapters, generated bridge adapters, and .agent-context/state/onboarding-report.json');
+      console.log('\nRefreshed files: AGENTS.md, CLAUDE.md, GEMINI.md, .agent-context/, and .agent-context/state/onboarding-report.json');
     } catch (error) {
       console.error('\n[FATAL] An error occurred during upgrade. Attempting automatic rollback...');
       try {

package/lib/cli/compiler.mjs

@@ -15,7 +15,6 @@ import {
 import {
   pathExists,
   collectFileNames,
-  isAgenticManagedContent,
 } from './utils.mjs';
 
 import {
@@ -106,38 +105,6 @@ function buildAnchorCommitmentHeader(designIntent) {
   ].join('\n');
 }
 
-function buildLegacyRootAdapterContent(adapterFileName, toolLabel) {
-  return [
-    `# ${adapterFileName} - Legacy Thin Adapter`,
-    '',
-    `Generated by Agentic-Senior-Core CLI v${CLI_VERSION}`,
-    'Adapter Mode: legacy-thin',
-    'Adapter Source: .agent-instructions.md when present; fallback .instructions.md',
-    'Canonical baseline: .instructions.md',
-    '',
-    `This file is kept only for older ${toolLabel} discovery.`,
-    'Read .agent-instructions.md for the compiled rulebook when present.',
-    'Use .instructions.md as the canonical policy source.',
-    '',
-    'Mandatory load floor:',
-    '1. Read .agent-instructions.md when present; otherwise read .instructions.md.',
-    '2. Load only relevant .agent-context/rules/ by task scope.',
-    '3. Apply matching .agent-context/prompts/ contracts.',
-    '4. Enforce .agent-context/review-checklists/ before completion.',
-    '5. Use .agent-context/state/ and .agent-context/policies/ only when relevant.',
-    '6. Resolve Runtime Decision Signals from repo evidence and live official docs.',
-    '7. Resolve Structural Planning Signals from constraints and architecture boundaries.',
-    '',
-    'Current bridges:',
-    '- Cursor: .cursor/rules/agentic-senior-core.mdc',
-    '- Windsurf: .windsurf/rules/agentic-senior-core.md',
-    '- Claude: CLAUDE.md',
-    '- Gemini: GEMINI.md and .gemini/instructions.md',
-    '- Copilot: .github/copilot-instructions.md and .github/instructions/agentic-senior-core.instructions.md',
-    '',
-  ].join('\n');
-}
-
 function buildContainerizationStrategySnapshot(dockerStrategy) {
   const selectedDockerStrategy = String(dockerStrategy || '').trim();
   const normalizedDockerStrategy = selectedDockerStrategy.toLowerCase();
@@ -220,7 +187,7 @@ export async function writeOnboardingReport({
     selectedBlueprint: hasExplicitArchitectureDecision ? selectedBlueprintFileName : null,
     selectedAdditionalBlueprints: hasExplicitArchitectureDecision ? selectedAdditionalBlueprintFileNames : [],
     ruleLoadingPolicy: {
-      canonicalSource: '.instructions.md',
+      canonicalSource: 'AGENTS.md',
       stackLoadingMode: 'lazy',
       domainRuleLoadingMode: 'lazy',
       loadedOnDemand: true,
@@ -330,11 +297,10 @@ export async function buildCompiledRulesContent({
       `6. .agent-context/policies/${POLICY_FILE_NAME}`,
       '7. docs/ project context (or bootstrap prompts when docs are not materialized)',
       '',
-      'Project-specific compiled snapshot: .agent-instructions.md',
-      'Compiled rulebook: .agent-instructions.md',
-      'Legacy thin root adapters: .cursorrules, .windsurfrules, .clauderc',
-      'Generated bridge adapters: AGENTS.md, CLAUDE.md, GEMINI.md, .cursor/rules/agentic-senior-core.mdc, .windsurf/rules/agentic-senior-core.md, .github/copilot-instructions.md, .github/instructions/agentic-senior-core.instructions.md, .gemini/instructions.md',
-      'Canonical baseline: .instructions.md',
+      'Canonical instruction source: AGENTS.md',
+      'Native import bridges: CLAUDE.md, GEMINI.md',
+      'Managed rule library: .agent-context/',
+      'Project decisions and dynamic state: .agent-context/state/onboarding-report.json',
     ].join('\n')
   );
 
@@ -659,62 +625,11 @@ export async function buildCompiledRulesContent({
     `Selected policy file: .agent-context/policies/${POLICY_FILE_NAME}`,
     '',
     '## GOVERNANCE PRECEDENCE',
-    '1. Follow this compiled rulebook as the primary source.',
-    '2. Resolve exceptions from .agent-override.md only when explicitly defined.',
-    '3. Use architecture-map.md and dependency-map.md as change safety boundaries.',
-    '4. Enforce pr-checklist.md before declaring completion.',
-    '',
-    '## OVERRIDE PROTOCOL',
-    '- Default: strict compliance with this file.',
-    '- Exception path: .agent-override.md may explicitly allow narrow deviations.',
-    '- Scope policy: every override must include module scope, rationale, and expiry date.',
+    '1. Follow AGENTS.md as the primary source.',
+    '2. Use architecture-map.md and dependency-map.md as change safety boundaries.',
+    '3. Enforce pr-checklist.md before declaring completion.',
     '',
     ...contextBlocks,
     '',
   ].join('\n');
 }
-
-export async function compileDynamicContext({
-  targetDirectoryPath,
-  selectedStackFileName,
-  selectedAdditionalStackFileNames = [],
-  selectedBlueprintFileName,
-  selectedAdditionalBlueprintFileNames = [],
-  includeCiGuardrails,
-  preserveUserOwnedEntrypoints = true,
-}) {
-  const resolvedTargetDirectoryPath = path.resolve(targetDirectoryPath);
-  const compiledRules = await buildCompiledRulesContent({
-    targetDirectoryPath: resolvedTargetDirectoryPath,
-    selectedStackFileName,
-    selectedAdditionalStackFileNames,
-    selectedBlueprintFileName,
-    selectedAdditionalBlueprintFileNames,
-    includeCiGuardrails,
-  });
-  const preservedEntrypoints = [];
-
-  async function writeGeneratedEntrypointFile(relativeFilePath, content) {
-    const targetFilePath = path.join(resolvedTargetDirectoryPath, relativeFilePath);
-
-    if (preserveUserOwnedEntrypoints && await pathExists(targetFilePath)) {
-      const existingContent = await fs.readFile(targetFilePath, 'utf8');
-      if (!isAgenticManagedContent(existingContent)) {
-        preservedEntrypoints.push(relativeFilePath);
-        return;
-      }
-    }
-
-    await fs.mkdir(path.dirname(targetFilePath), { recursive: true });
-    await fs.writeFile(targetFilePath, content, 'utf8');
-  }
-
-  await fs.writeFile(path.join(resolvedTargetDirectoryPath, '.agent-instructions.md'), compiledRules, 'utf8');
-  await writeGeneratedEntrypointFile('.cursorrules', buildLegacyRootAdapterContent('.cursorrules', 'Cursor'));
-  await writeGeneratedEntrypointFile('.windsurfrules', buildLegacyRootAdapterContent('.windsurfrules', 'Windsurf'));
-  await writeGeneratedEntrypointFile('.clauderc', buildLegacyRootAdapterContent('.clauderc', 'Claude'));
-
-  return {
-    preservedEntrypoints,
-  };
-}

package/lib/cli/constants.mjs

@@ -126,19 +126,11 @@ export const RUNTIME_ENVIRONMENT_CHOICES = [
 ];
 
 export const entryPointFiles = [
-  '.instructions.md',
-  '.cursorrules',
-  '.windsurfrules',
   'AGENTS.md',
   'CLAUDE.md',
   'GEMINI.md',
-  '.cursor/rules/agentic-senior-core.mdc',
-  '.github/copilot-instructions.md',
-  '.github/instructions/agentic-senior-core.instructions.md',
-  '.windsurf/rules/agentic-senior-core.md',
-  '.agent-override.md',
 ];
 
-export const directoryCopies = ['.agent-context', '.gemini', '.agents'];
+export const directoryCopies = ['.agent-context'];
 
 export const BACKUP_DIR_NAME = '.agentic-backup';

package/lib/cli/detector.mjs

@@ -102,7 +102,6 @@ const PROJECT_MARKER_FILE_NAMES = new Set([
 const INTERNAL_GOVERNANCE_SURFACE_NAMES = new Set([
   '.agent-context',
   '.agent-instructions.md',
-  '.agent-override.md',
   '.agentic-backup',
   '.agents',
   '.clauderc',

package/lib/cli/init-options.mjs

@@ -23,7 +23,7 @@ export function parseInitArguments(commandArguments) {
     tokenOptimize: true,
     memoryContinuity: true,
     tokenAgent: 'copilot',
-    includeMcpTemplate: true,
+    includeMcpTemplate: false,
     scaffoldDocs: undefined,
     docsLang: 'en',
     docsLangProvided: false,

package/lib/cli/utils/filesystem.mjs

@@ -51,6 +51,8 @@ export function isAgenticManagedContent(content) {
     'Adapter Mode: legacy-thin',
     'Canonical Snapshot SHA256',
     'Canonical baseline: .instructions.md',
+    'canonical instruction source for this repository',
+    '@AGENTS.md',
   ].some((managedSignal) => normalizedContent.includes(managedSignal));
 }
 

package/lib/cli/utils/managed-surface.mjs

@@ -6,7 +6,10 @@ import {
   entryPointFiles,
   directoryCopies,
 } from '../constants.mjs';
-import { pathExists } from './filesystem.mjs';
+import {
+  isAgenticManagedContent,
+  pathExists,
+} from './filesystem.mjs';
 
 function toPosixRelativePath(relativePath) {
   return relativePath.split(path.sep).join('/');
@@ -29,6 +32,34 @@ const localOnlyGovernanceFiles = new Set([
   '.agent-context/state/v3-purge-audit.json',
 ]);
 
+const legacyManagedInstructionFiles = [
+  '.instructions.md',
+  '.agent-instructions.md',
+  '.cursorrules',
+  '.windsurfrules',
+  '.clauderc',
+  '.cursor/rules/agentic-senior-core.mdc',
+  '.windsurf/rules/agentic-senior-core.md',
+  '.github/copilot-instructions.md',
+  '.github/instructions/agentic-senior-core.instructions.md',
+  '.gemini/instructions.md',
+  '.agents/workflows/init-project.md',
+  '.agents/workflows/refactor.md',
+  '.agents/workflows/review-code.md',
+];
+
+export const legacyManagedInstructionDirectories = [
+  '.agents/workflows',
+  '.agents',
+  '.cursor/rules',
+  '.cursor',
+  '.windsurf/rules',
+  '.windsurf',
+  '.github/instructions',
+  '.github',
+  '.gemini',
+];
+
 function isLocalOnlyGovernanceFile(relativePath) {
   return localOnlyGovernanceFiles.has(toPosixRelativePath(relativePath));
 }
@@ -171,6 +202,18 @@ async function collectManagedTargetManifest(resolvedTargetDirectoryPath, options
     targetDirectories.add(targetDirectoryPath);
   }
 
+  for (const legacyManagedFile of legacyManagedInstructionFiles) {
+    const targetFilePath = path.join(resolvedTargetDirectoryPath, ...legacyManagedFile.split('/'));
+    if (!(await pathExists(targetFilePath))) {
+      continue;
+    }
+
+    const targetFileContent = await fs.readFile(targetFilePath);
+    if (isAgenticManagedContent(targetFileContent)) {
+      targetFiles.add(legacyManagedFile);
+    }
+  }
+
   return {
     files: targetFiles,
     directories: targetDirectories,
@@ -183,7 +226,7 @@ export async function analyzeManagedGovernanceSurface(
 ) {
   const preservePathPrefixes = Array.isArray(options.preservePathPrefixes)
     ? options.preservePathPrefixes
-    : ['.agent-context/state', '.gemini'];
+    : ['.agent-context/state'];
 
   const sourceManifest = await buildManagedSourceManifest(options);
   const targetManifest = await collectManagedTargetManifest(resolvedTargetDirectoryPath, options);

package/lib/cli/utils.mjs

@@ -22,6 +22,7 @@ import {
 import {
   collectRelativeTreeEntries,
   analyzeManagedGovernanceSurface,
+  legacyManagedInstructionDirectories,
 } from './utils/managed-surface.mjs';
 export {
   pathExists,
@@ -32,6 +33,7 @@ export {
 } from './utils/filesystem.mjs';
 export {
   analyzeManagedGovernanceSurface,
+  legacyManagedInstructionDirectories,
 } from './utils/managed-surface.mjs';
 export {
   askChoice,
@@ -71,8 +73,8 @@ export function printUsage() {
   console.log('  --no-token-optimize  Disable token optimization policy during init');
   console.log('  --memory-continuity  Explicitly enable cross-session memory continuity policy during init (default behavior)');
   console.log('  --no-memory-continuity  Disable memory continuity policy during init');
-  console.log('  --mcp-template   Explicitly enable cross-IDE MCP auto-configuration (default behavior)');
-  console.log('  --no-mcp-template Disable automatic MCP configuration across your IDEs');
+  console.log('  --mcp-template   Explicitly enable cross-IDE MCP auto-configuration (opt-in)');
+  console.log('  --no-mcp-template Keep MCP configuration disabled (default behavior)');
   console.log('  --scaffold-docs  Force project documentation scaffolding (architecture, database, API, flow)');
   console.log('  --no-scaffold-docs  Skip project documentation scaffolding');
   console.log('  --docs-lang      Optional override for bootstrap docs synthesis language (default: en)');
@@ -83,8 +85,8 @@ export function printUsage() {
   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');
+  console.log('  --enable     Enable token optimization policy state');
+  console.log('  --disable    Disable token optimization policy state');
   console.log('  --show       Print current token optimization state as JSON');
 }
 
@@ -125,6 +127,17 @@ async function syncMcpConfig(mcpJsonPath, templateConfig) {
   }
 }
 
+async function pruneEmptyLegacyInstructionDirectories(resolvedTargetDirectoryPath) {
+  for (const relativeDirectoryPath of legacyManagedInstructionDirectories) {
+    const directoryPath = path.join(resolvedTargetDirectoryPath, ...relativeDirectoryPath.split('/'));
+    try {
+      await fs.rmdir(directoryPath);
+    } catch {
+      // Keep non-empty or missing directories. They may contain user-owned files.
+    }
+  }
+}
+
 export async function copyGovernanceAssetsToTarget(
   resolvedTargetDirectoryPath,
   options = {}
@@ -205,6 +218,8 @@ export async function copyGovernanceAssetsToTarget(
       await fs.rm(staleDirectoryPath, { recursive: true, force: true });
       deletedManagedDirectories.push(staleDirectoryRelativePath);
     }
+
+    await pruneEmptyLegacyInstructionDirectories(resolvedTargetDirectoryPath);
   }
 
   if (shouldIncludeMcpTemplate) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ryuenn3123/agentic-senior-core",
-  "version": "3.0.47",
+  "version": "3.0.48",
   "type": "module",
   "description": "Force your AI Agent to code like a Staff Engineer, not a Junior.",
   "bin": {
@@ -10,7 +10,6 @@
     "bin/",
     "lib/",
     "scripts/",
-    ".instructions.md",
     ".agent-context/policies/",
     ".agent-context/prompts/",
     ".agent-context/review-checklists/",
@@ -24,17 +23,9 @@
     ".agent-context/state/benchmark-writer-judge-config.json",
     ".agent-context/state/memory-adapter-contract.json",
     ".agent-context/state/memory-schema-v1.json",
-    ".agents/",
-    ".cursor/",
-    ".github/",
-    ".gemini/",
-    ".windsurf/",
-    ".cursorrules",
-    ".windsurfrules",
     "AGENTS.md",
     "CLAUDE.md",
     "GEMINI.md",
-    ".agent-override.md",
     "mcp.json",
     "README.md",
     "LICENSE",

package/scripts/bump-version.mjs

@@ -71,22 +71,7 @@ async function bumpVersion() {
     console.log('Updated docs/deep-analysis-and-roadmap-backlog.md');
   }
 
-  // 4. Update legacy root adapters that carry release metadata.
-  const legacyAdapterFiles = ['.cursorrules', '.windsurfrules'];
-  for (const legacyAdapterFile of legacyAdapterFiles) {
-    const legacyAdapterPath = path.join(ROOT_DIR, legacyAdapterFile);
-    if (await fileExists(legacyAdapterPath)) {
-      const legacyAdapterContent = await readTextFile(legacyAdapterPath);
-      const updatedLegacyAdapterContent = legacyAdapterContent.replace(
-        /Generated by Agentic-Senior-Core CLI v\d+\.\d+\.\d+/,
-        `Generated by Agentic-Senior-Core CLI v${newVersion}`
-      );
-      await writeTextFile(legacyAdapterPath, updatedLegacyAdapterContent);
-      console.log(`Updated ${legacyAdapterFile}`);
-    }
-  }
-
-  // 5. Update CHANGELOG.md
+  // 4. Update CHANGELOG.md
   const changelogPath = path.join(ROOT_DIR, 'CHANGELOG.md');
   if (await fileExists(changelogPath)) {
     let changelogContent = await readTextFile(changelogPath);

package/scripts/docs-quality-drift-report.mjs

@@ -24,15 +24,9 @@ const LONG_SENTENCE_WORD_THRESHOLD = 28;
 const MONITORED_STATIC_FILE_PATHS = [
   'README.md',
   'CHANGELOG.md',
-  '.instructions.md',
   'AGENTS.md',
   'CLAUDE.md',
   'GEMINI.md',
-  '.github/copilot-instructions.md',
-  '.github/instructions/agentic-senior-core.instructions.md',
-  '.gemini/instructions.md',
-  '.cursor/rules/agentic-senior-core.mdc',
-  '.windsurf/rules/agentic-senior-core.md',
   'docs/deep-analysis-and-roadmap-backlog.md',
 ];
 

package/scripts/frontend-usability-audit.mjs

@@ -20,7 +20,7 @@ const REQUIRED_FILES = [
   'docs/roadmap.md',
   'docs/archive/v1.7-issue-breakdown.md',
   'docs/archive/v1.7-execution-playbook.md',
-  '.instructions.md',
+  'AGENTS.md',
   '.agent-context/prompts/bootstrap-design.md',
   'scripts/ui-design-judge.mjs',
   'scripts/ui-rubric-calibration.mjs',
@@ -173,7 +173,7 @@ function runAudit() {
   const roadmapPath = 'docs/roadmap.md';
   const frontendRulePath = '.agent-context/rules/frontend-architecture.md';
   const bootstrapDesignPromptPath = '.agent-context/prompts/bootstrap-design.md';
-  const instructionsPath = '.instructions.md';
+  const instructionsPath = 'AGENTS.md';
   const prChecklistPath = '.agent-context/review-checklists/pr-checklist.md';
   const architectureChecklistPath = '.agent-context/review-checklists/architecture-review.md';
   const designEvidenceExtractorPath = 'lib/cli/detector/design-evidence.mjs';

package/scripts/governance-weekly-report.mjs

@@ -44,7 +44,7 @@ const REQUIRED_VERIFIED_DOMAINS = new Set([
   'state-continuity',
 ]);
 const GOVERNANCE_SURFACE_PATHS = {
-  'canonical-instructions': '.instructions.md',
+  'canonical-instructions': 'AGENTS.md',
   'frontend-design-contract': '.agent-context/prompts/bootstrap-design.md',
   'frontend-architecture': '.agent-context/rules/frontend-architecture.md',
   'backend-architecture': '.agent-context/rules/architecture.md',
@@ -75,7 +75,7 @@ const BACKEND_GOVERNANCE_COVERAGE = [
     constraint: 'Global backend/API rule routing',
     status: 'strengthened',
     sourcePaths: [
-      '.instructions.md',
+      'AGENTS.md',
       '.agent-context/rules/architecture.md',
       '.agent-context/prompts/refactor.md',
     ],