diff --git a/scripts/lib/install-lifecycle.js b/scripts/lib/install-lifecycle.js
index ec9cb1d80..b2f967b91 100644
--- a/scripts/lib/install-lifecycle.js
+++ b/scripts/lib/install-lifecycle.js
@@ -13,6 +13,10 @@ const { getRecordedHookConsent } = require('./install/hook-consent');
 const {
   prepareClaudeSkillMigration,
 } = require('./install/claude-skill-migration');
+const {
+  prepareLegacyAgentsMigration,
+  removeLegacyAgentsFiles,
+} = require('./install/legacy-agents-migration');
 const {
   getLegacyAntigravityLocation,
   inspectLegacyAntigravityState,
@@ -1908,7 +1912,10 @@ function prepareRepairMigration(plan, record) {
     installStatePath: record.installStatePath,
     statePreview: buildAdapterDerivedStatePreview(plan.statePreview, record),
   };
-  const migration = prepareClaudeSkillMigration(trustedPlan);
+  const migration = prepareLegacyAgentsMigration(
+    trustedPlan,
+    prepareClaudeSkillMigration(trustedPlan)
+  );
   return {
     migration,
     plan: {
@@ -2131,10 +2138,16 @@ function repairInstalledStates(options = {}) {
       const legacyMigrationPaths = migration.legacyOperationsToRemove.map(
         operation => operation.destinationPath
       );
+      const legacyAgentsMigrationPaths = migration.legacyAgentsOperationsToRemove.map(
+        operation => operation.destinationPath
+      );
+      const hasLegacyAgentsStateMigration = migration.legacyAgentsOperationsToDetach.length > 0;
       const plannedRepairs = [...new Set([
         ...(needsOpencodeBuild ? [opencodeBuildRepairPath] : []),
         ...repairOperations.map(operation => operation.destinationPath),
         ...legacyMigrationPaths,
+        ...legacyAgentsMigrationPaths,
+        ...(hasLegacyAgentsStateMigration ? [record.installStatePath] : []),
       ])];
 
       if (options.dryRun) {
@@ -2150,7 +2163,8 @@ function repairInstalledStates(options = {}) {
         };
       }
 
-      const hasLegacyMigration = migration.legacyOperationsToRemove.length > 0;
+      const hasLegacyMigration = migration.legacyOperationsToRemove.length > 0
+        || hasLegacyAgentsStateMigration;
       const repairedPaths = needsOpencodeBuild ? [opencodeBuildRepairPath] : [];
       if (migration.requiresBridgeState && (repairOperations.length > 0 || hasLegacyMigration)) {
         writeRefreshedInstallState(record, migration.bridgeState);
@@ -2181,6 +2195,8 @@ function repairInstalledStates(options = {}) {
             repairedPaths.push(removedPath);
           }
         }
+        removeLegacyAgentsFiles(migration, record.targetRoot);
+        repairedPaths.push(...legacyAgentsMigrationPaths.filter(filePath => !fs.existsSync(filePath)));
       }
       const changedInstalledBytes = repairOperations.length > 0
         || needsOpencodeBuild
diff --git a/scripts/lib/install/apply.js b/scripts/lib/install/apply.js
index fbab1293b..7ecc05fa0 100644
--- a/scripts/lib/install/apply.js
+++ b/scripts/lib/install/apply.js
@@ -22,6 +22,10 @@ const {
 } = require('./claude-settings');
 const { filterMcpConfig, parseDisabledMcpServers } = require('../mcp-config');
 const { assertWithinTrustedRoot } = require('../path-safety');
+const {
+  prepareLegacyAgentsMigration,
+  removeLegacyAgentsFiles,
+} = require('./legacy-agents-migration');
 const {
   assertSafeClaudeSkillOperation,
   prepareClaudeSkillMigration,
@@ -398,7 +402,10 @@ function prepareHookConsentMigration(plan, migration) {
 function previewInstallPlan(plan) {
   const migration = prepareHookConsentMigration(
     plan,
-    prepareUserOwnedFileGuard(plan, prepareClaudeSkillMigration(plan))
+    prepareUserOwnedFileGuard(
+      plan,
+      prepareLegacyAgentsMigration(plan, prepareClaudeSkillMigration(plan))
+    )
   );
   const appliedPlan = {
     ...plan,
@@ -451,7 +458,10 @@ function applyInstallPlanLocked(plan, dependencies = {}, settingsLockHeld = fals
   }
   const migration = prepareHookConsentMigration(
     plan,
-    prepareUserOwnedFileGuard(plan, prepareClaudeSkillMigration(plan))
+    prepareUserOwnedFileGuard(
+      plan,
+      prepareLegacyAgentsMigration(plan, prepareClaudeSkillMigration(plan))
+    )
   );
   const appliedPlan = {
     ...plan,
@@ -590,6 +600,7 @@ function applyInstallPlanLocked(plan, dependencies = {}, settingsLockHeld = fals
       if (hasLegacyMigration) {
         removeLegacyClaudeSkillFiles(migration, plan.targetRoot);
       }
+      removeLegacyAgentsFiles(migration, plan.targetRoot);
 
       if (shouldSetClaudeCommitAttributionPreference(appliedPlan)) {
         writeClaudeCommitAttributionPreference(
diff --git a/scripts/lib/install/legacy-agents-migration.js b/scripts/lib/install/legacy-agents-migration.js
new file mode 100644
index 000000000..1e613da83
--- /dev/null
+++ b/scripts/lib/install/legacy-agents-migration.js
@@ -0,0 +1,172 @@
+'use strict';
+
+const crypto = require('crypto');
+const fs = require('fs');
+const path = require('path');
+
+const { readInstallState } = require('../install-state');
+const { assertWithinTrustedRoot } = require('../path-safety');
+
+const HOME_TARGET_IDS = new Set(['claude-home', 'codex-home']);
+
+function comparablePath(filePath) {
+  const resolvedPath = path.resolve(filePath);
+  return process.platform === 'win32' ? resolvedPath.toLowerCase() : resolvedPath;
+}
+
+function normalizeRelativePath(relativePath) {
+  return String(relativePath || '').replace(/\\/g, '/');
+}
+
+function isLegacyAgentsOperation(plan, operation) {
+  if (
+    !operation
+    || operation.kind !== 'copy-file'
+    || operation.ownership !== 'managed'
+    || typeof operation.destinationPath !== 'string'
+  ) {
+    return false;
+  }
+
+  const sourceRelativePath = normalizeRelativePath(operation.sourceRelativePath);
+  if (!sourceRelativePath.startsWith('.agents/')) {
+    return false;
+  }
+
+  const expectedDestination = path.join(
+    plan.targetRoot,
+    ...sourceRelativePath.split('/')
+  );
+  return comparablePath(operation.destinationPath) === comparablePath(expectedDestination);
+}
+
+function inspectLegacyAgentsOperation(plan, operation) {
+  assertWithinTrustedRoot(
+    operation.destinationPath,
+    plan.targetRoot,
+    'inspect legacy managed .agents file'
+  );
+
+  let stat;
+  try {
+    stat = fs.lstatSync(operation.destinationPath);
+  } catch (error) {
+    if (error && error.code === 'ENOENT') {
+      return { removable: false, warning: null };
+    }
+    throw error;
+  }
+
+  if (!stat.isFile() || stat.isSymbolicLink()) {
+    return {
+      removable: false,
+      warning: `Preserved legacy .agents path ${operation.destinationPath}: it is not a regular file.`,
+    };
+  }
+
+  if (!/^[a-f0-9]{64}$/i.test(operation.contentSha256 || '')) {
+    return {
+      removable: false,
+      warning: `Preserved legacy .agents file ${operation.destinationPath}: install-state has no verified content digest.`,
+    };
+  }
+
+  const contentSha256 = crypto.createHash('sha256')
+    .update(fs.readFileSync(operation.destinationPath))
+    .digest('hex');
+  if (contentSha256 !== operation.contentSha256.toLowerCase()) {
+    return {
+      removable: false,
+      warning: `Preserved modified legacy .agents file ${operation.destinationPath} and released it from ECC management.`,
+    };
+  }
+
+  return { removable: true, warning: null };
+}
+
+function prepareLegacyAgentsMigration(plan, migration) {
+  if (!HOME_TARGET_IDS.has(plan && plan.adapter && plan.adapter.id)) {
+    return {
+      ...migration,
+      legacyAgentsOperationsToDetach: [],
+      legacyAgentsOperationsToRemove: [],
+    };
+  }
+
+  const previousState = fs.existsSync(plan.installStatePath)
+    ? readInstallState(plan.installStatePath)
+    : null;
+  const legacyOperations = ((previousState && previousState.operations) || [])
+    .filter(operation => isLegacyAgentsOperation(plan, operation));
+  if (legacyOperations.length === 0) {
+    return {
+      ...migration,
+      legacyAgentsOperationsToDetach: [],
+      legacyAgentsOperationsToRemove: [],
+    };
+  }
+
+  const inspections = legacyOperations.map(operation => ({
+    operation,
+    ...inspectLegacyAgentsOperation(plan, operation),
+  }));
+  const legacyDestinations = new Set(
+    legacyOperations.map(operation => comparablePath(operation.destinationPath))
+  );
+  const withoutLegacyAgents = state => ({
+    ...state,
+    operations: (state.operations || []).filter(operation => (
+      !legacyDestinations.has(comparablePath(operation.destinationPath))
+    )),
+  });
+
+  return {
+    ...migration,
+    finalState: withoutLegacyAgents(migration.finalState),
+    legacyAgentsOperationsToDetach: legacyOperations,
+    legacyAgentsOperationsToRemove: inspections
+      .filter(inspection => inspection.removable)
+      .map(inspection => inspection.operation),
+    requiresBridgeState: true,
+    warnings: [
+      ...(migration.warnings || []),
+      ...inspections.map(inspection => inspection.warning).filter(Boolean),
+    ],
+  };
+}
+
+function cleanupEmptyAgentsParents(filePath, targetRoot) {
+  const agentsRoot = path.join(targetRoot, '.agents');
+  let currentPath = path.dirname(filePath);
+
+  while (comparablePath(currentPath) !== comparablePath(targetRoot)) {
+    assertWithinTrustedRoot(currentPath, targetRoot, 'clean legacy managed .agents directory');
+    if (!fs.existsSync(currentPath) || fs.readdirSync(currentPath).length > 0) {
+      return;
+    }
+    fs.rmdirSync(currentPath);
+    if (comparablePath(currentPath) === comparablePath(agentsRoot)) {
+      return;
+    }
+    currentPath = path.dirname(currentPath);
+  }
+}
+
+function removeLegacyAgentsFiles(migration, targetRoot) {
+  for (const operation of migration.legacyAgentsOperationsToRemove || []) {
+    const latestInspection = inspectLegacyAgentsOperation(
+      { targetRoot },
+      operation
+    );
+    if (!latestInspection.removable) {
+      continue;
+    }
+    fs.rmSync(operation.destinationPath, { force: true });
+    cleanupEmptyAgentsParents(operation.destinationPath, targetRoot);
+  }
+}
+
+module.exports = {
+  prepareLegacyAgentsMigration,
+  removeLegacyAgentsFiles,
+};