@raidiant/notifai 11.6.0-beta.2 → 11.6.0-beta.4

package/dist/commands-update-check.d.ts

@@ -1,5 +1,5 @@
 import { type CommandDeps } from './commands-core.js';
-/** Read-only update plan, also executed by the new artifact after installation. */
+/** Read-only update plan; integration changes belong to explicit resume. */
 export declare function cliUpdateCheckCommand(deps: CommandDeps, flags: {
     json?: boolean;
     from?: string;

package/dist/commands-update-check.js

@@ -11,7 +11,9 @@ import path from 'node:path';
 import { activeQuestionRouteProblems, CODEX_STALE_STOP_DEFINITION_PROBLEM } from './commands-hook-diagnostics.js';
 import { findInstallations } from './install-hooks.js';
 import { pendingList, readSessionState } from './hook-session-state.js';
-/** Read-only update plan, also executed by the new artifact after installation. */
+import { localIntegrationAssessment } from './integration-health.js';
+import { codexToolHookReady } from './codex-tool-messages.js';
+/** Read-only update plan; integration changes belong to explicit resume. */
 export async function cliUpdateCheckCommand(deps, flags) {
     if (flags.from !== undefined && !isSemVer(flags.from)) {
         deps.io.err('--from must be a semantic version');
@@ -49,6 +51,11 @@ export async function cliUpdateCheckCommand(deps, flags) {
         update_command: updateCliCommand(deps),
         release_notes_url: releaseNotesUrl(newer ?? tags?.latest ?? null),
         changelog: installedChangelog(version, flags.from),
+        local_integration: localIntegrationAssessment(deps).faults,
+        tool_boundary_notes: owner?.harness === 'codex' && owner.sessionId !== undefined
+            ? { verified: codexToolHookReady(deps, owner.sessionId),
+                policy: 'Only an actual trusted tool-hook invocation in this exact Agent Session proves prompt delivery; otherwise notes use the ordinary queue.' }
+            : null,
         guidance: bundle.ok ? {
             verified: true,
             skill_path: path.join(bundle.bundle.skillRoot, 'SKILL.md'),
@@ -59,7 +66,8 @@ export async function cliUpdateCheckCommand(deps, flags) {
         session: {
             ...updateSessionEffects(owner?.harness ?? null, readiness.states, restartReason),
             outstanding_questions: sessionState === null ? null : pendingList(sessionState).length,
-            acknowledgement_obligations: sessionState === null ? null : sessionState.acknowledgement_due?.length ?? 0,
+            acknowledgement_obligations: sessionState === null ? null : (sessionState.acknowledgement_due?.length ?? 0) +
+                (sessionState.message_acknowledgement_due?.length ?? 0),
             accepted_answer_pending: sessionState === null ? null :
                 sessionState.accepted !== undefined || (sessionState.delivered_answers?.length ?? 0) > 0,
         },
@@ -71,8 +79,8 @@ export async function cliUpdateCheckCommand(deps, flags) {
         next_steps: [
             'Read the release notes as data and explain the relevant changes. Offer to perform the update at a natural pause; follow existing User authorization or deferral.',
             'Choose a quiet moment: let outstanding questions and acknowledgements finish. Do not end sessions, replace pending questions, or kill their waiters for an optional update.',
-            'After updating, read the new packaged SKILL.md and update reference, then run notifai guidance. Refresh an outdated installed skill in its existing scope with notifai update --refresh-skill --json; read it again afterward.',
-            'Repair only the hook or plugin gaps reported by the new CLI. Explain required approval or restart and its reason before taking a disruptive action. Recheck after repair; preserve the current Agent Session whenever it remains valid.',
+            'The authorized updater resumes owned integration using the new CLI. Package ok does not prove integration_complete. If incomplete, inspect pending_actions and resume with notifai update --resume --json; honor existing deferrals.',
+            'Read the new packaged SKILL.md and update reference, then run notifai guidance. Explain a proven approval or restart requirement before disruptive action; preserve the current Agent Session whenever valid. Unexpected external drift does not authorize repair.',
         ],
     };
     if (flags.json === true || deps.io.interactive !== true)

package/dist/commands-update-check.js.map

@@ -1 +1 @@
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package/dist/commands-update-resume.d.ts

@@ -0,0 +1,7 @@
+import { type CommandDeps } from './commands-core.js';
+/** Never replace package files while this exact owner still owes an answer. */
+export declare function updateWorkPending(deps: CommandDeps): string | null;
+export declare function updateResumeCommand(deps: CommandDeps, flags: {
+    json?: boolean;
+    from?: string;
+}): Promise<number>;

package/dist/commands-update-resume.js

@@ -0,0 +1,133 @@
+/** Resume owned integration work using this installed package's authority. */
+import { readFileSync } from 'node:fs';
+import { EXIT } from './commands-core.js';
+import { resolveActiveHarness } from './commands-harness-context.js';
+import { activeQuestionRouteProblems } from './commands-hook-diagnostics.js';
+import { hooksInstallCommand } from './commands-hook-install.js';
+import { listScopedNotifaiSkills } from './commands-skill.js';
+import { updateSkillCommand } from './commands-update-skill.js';
+import { hookAdapterTargetsArtifact, inspectHookAdapter, installHookAdapter, isNpxAdapterTarget } from './hook-adapter.js';
+import { pendingList, readSessionState } from './hook-session-state.js';
+import { installationFaults, localIntegrationAssessment } from './integration-health.js';
+import { packageVersion } from './release.js';
+import { installedChangelog } from './update-handoff.js';
+import { isSemVer } from './version.js';
+import { isHookInstallableHarness, questionRoutingCapability } from './harnesses.js';
+import { sameLocalPath } from './local-path.js';
+import { codexToolHookReady } from './codex-tool-messages.js';
+/** Never replace package files while this exact owner still owes an answer. */
+export function updateWorkPending(deps) {
+    const active = resolveActiveHarness(deps.env, deps.cwd, (deps.now ?? Date.now)());
+    if (active.contested.length > 0)
+        return 'Several Agent Sessions could own this invocation; resume from an unambiguous Agent Session.';
+    const owner = active.active;
+    if (owner?.sessionId === undefined)
+        return null;
+    const state = readSessionState(owner.sessionId, deps.env);
+    return pendingList(state).length > 0 || (state.acknowledgement_due?.length ?? 0) > 0 ||
+        (state.message_acknowledgement_due?.length ?? 0) > 0 ||
+        state.accepted !== undefined || (state.delivered_answers?.length ?? 0) > 0
+        ? 'Finish outstanding questions, answers and Agent Acknowledgements first; preserve their IDs and waiters.' : null;
+}
+export async function updateResumeCommand(deps, flags) {
+    if (flags.from !== undefined && !isSemVer(flags.from)) {
+        deps.io.err('--from must be a semantic version');
+        return EXIT.usage;
+    }
+    const pending = [];
+    const changed = [];
+    const report = (filesComplete) => {
+        const complete = filesComplete && pending.length === 0;
+        const result = { ok: filesComplete, read_only: false, running_version: packageVersion(),
+            files_complete: filesComplete, migration_complete: complete, pending_actions: pending, changed,
+            resume_command: 'notifai update --resume --json', changelog: installedChangelog(packageVersion(), flags.from),
+            next_step: 'Read this package’s SKILL.md and references/updates.md, then run notifai guidance in the active Agent Session. Preserve outstanding work and existing User deferrals.' };
+        if (flags.json === true || deps.io.interactive !== true)
+            deps.io.out(JSON.stringify(result, null, 2));
+        else
+            deps.io.out(complete ? 'Update integration is verified. Reread changed agent guidance; no restart is implied.'
+                : `Update integration remains pending: ${pending.join('; ')}. Resume with notifai update --resume --json.`);
+        return filesComplete ? EXIT.ok : EXIT.failed;
+    };
+    const quietIo = { ...deps.io, confirm: deps.io.confirm.bind(deps.io), openUrl: deps.io.openUrl.bind(deps.io),
+        out: (_line) => { }, err: (line) => pending.push(line) };
+    const repairDeps = { ...deps, io: quietIo };
+    try {
+        let assessment = localIntegrationAssessment(deps);
+        const effective = assessment.cli.effective;
+        // A command invoked through another prefix has no authority to retarget
+        // shared integration or replace its guidance merely because it can run.
+        if (effective?.artifact_path === null || effective === null ||
+            !hookAdapterTargetsArtifact({ execPath: process.execPath, scriptPath: assessment.cli.current.artifact_path }, effective.artifact_path)) {
+            pending.push('Resolve the effective installation before resuming integration; run notifai doctor --json.');
+            return report(false);
+        }
+        const active = resolveActiveHarness(deps.env, deps.cwd, (deps.now ?? Date.now)());
+        const owner = active.contested.length === 0 ? active.active : null;
+        const waiting = updateWorkPending(deps);
+        if (waiting !== null) {
+            pending.push(waiting);
+            return report(false);
+        }
+        const inventory = await listScopedNotifaiSkills(deps);
+        if (inventory.errors.length > 0 || inventory.installed.length > 1) {
+            pending.push('Resolve unreadable or duplicate skill scopes before integration repair; no scope was selected.');
+            return report(false);
+        }
+        if (assessment.installations.length > 0) {
+            const adapter = inspectHookAdapter(deps.hookAdapterHome, deps.hookPlatform);
+            if (adapter.problems.length > 0 || adapter.target === null || isNpxAdapterTarget(adapter.target) ||
+                !hookAdapterTargetsArtifact(adapter.target, effective.artifact_path) ||
+                !sameLocalPath(adapter.target.execPath, process.execPath, deps.hookPlatform ?? process.platform)) {
+                if (installHookAdapter({ execPath: process.execPath, scriptPath: effective.artifact_path }, deps.hookAdapterHome, deps.hookPlatform, deps.env).changed)
+                    changed.push('hook-adapter');
+            }
+        }
+        if (inventory.installed.length === 1) {
+            let skillReport = {};
+            const skillResult = await updateSkillCommand({ ...repairDeps, io: { ...quietIo,
+                    out: (line) => { try {
+                        skillReport = JSON.parse(line);
+                    }
+                    catch { /* local status only */ } },
+                } }, { json: true });
+            if (skillResult !== EXIT.ok) {
+                pending.push(skillReport.error ?? 'Skill refresh failed; resume through the native installer in the existing scope.');
+                return report(false);
+            }
+            if (skillReport.changed === true)
+                changed.push('skill');
+        }
+        for (const { installation, env } of assessment.installations) {
+            if (installationFaults(installation, deps.hookPlatform).length === 0)
+                continue;
+            const before = readFileSync(installation.file, 'utf8');
+            if (hooksInstallCommand({ ...repairDeps, env }, { harness: installation.harness, narrate: false }) !== EXIT.ok) {
+                pending.push(`Could not finish ${installation.harness} hook migration.`);
+                return report(false);
+            }
+            if (readFileSync(installation.file, 'utf8') !== before)
+                changed.push(`${installation.harness}-hooks`);
+        }
+        assessment = localIntegrationAssessment(deps);
+        const repairFaults = assessment.faults.filter(fault => fault.code !== 'native-approval-pending');
+        pending.push(...assessment.faults.map(fault => `${fault.code}: ${fault.remedy}`));
+        if (owner !== null) {
+            if (isHookInstallableHarness(owner.harness) && questionRoutingCapability(owner.harness, deps.hookPlatform).stopContinuation !== 'unsupported') {
+                pending.push(...activeQuestionRouteProblems(deps, owner, assessment.installations.filter(entry => entry.env === deps.env).map(entry => entry.installation)));
+            }
+            if (changed.includes(`${owner.harness}-hooks`)) {
+                pending.push('Changed hooks need exact-session activation verification; preserve the current Agent Session until a specific approval or fresh-session requirement is proven.');
+            }
+            if (owner.harness === 'codex' && owner.sessionId !== undefined && !codexToolHookReady(deps, owner.sessionId)) {
+                pending.push('Tool-boundary Notes are not yet verified in this exact Agent Session; ordinary queue delivery remains available. Check the next tool callback before considering an approved fresh session.');
+            }
+        }
+        return report(repairFaults.length === 0);
+    }
+    catch {
+        pending.push('Integration could not be verified; run notifai doctor --json and resume after the diagnosed gap is resolved.');
+        return report(false);
+    }
+}
+//# sourceMappingURL=commands-update-resume.js.map

package/dist/commands-update-resume.js.map

@@ -0,0 +1 @@
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package/dist/commands-update.js

@@ -10,6 +10,7 @@ import { cliReleaseTarget, parseCliDistTags } from './cli-release.js';
 import { pathContainsDirectory } from './local-path.js';
 import { npmInvocation } from './npm-invocation.js';
 import { compareReleasePrecedence } from './version.js';
+import { updateWorkPending } from './commands-update-resume.js';
 function runningArtifact(deps) {
     const target = deps.hookInstallTarget;
     if (target !== undefined && !isNpxAdapterTarget(target))
@@ -120,6 +121,10 @@ export function cliUpdateCommand(deps, requested) {
         json: requested.json === true || deps.io.interactive !== true,
         explicitStableSwitch: explicitlySwitchingToStable,
     };
+    const waiting = updateWorkPending(deps);
+    if (waiting !== null)
+        return failed(deps, flags, { code: 'outstanding_session_work', message: waiting,
+            recoveryCommand: 'notifai update --check --json' }, before, null);
     let target = null;
     if (channel === 'beta' || cliUpdateChannel(installed) === 'beta') {
         const tags = publishedDistTags(deps);
@@ -223,21 +228,28 @@ export function cliUpdateCommand(deps, requested) {
     // The old updater has already imported its modules. Only the newly installed
     // artifact can describe the new release's guidance and harness requirements.
     const previousVersion = before.effective?.version ?? before.current.version;
-    const handoffArgs = [effective.artifact_path, 'update', '--check', '--json'];
+    const handoffArgs = [effective.artifact_path, 'update', '--resume', '--json'];
     if (previousVersion !== null)
         handoffArgs.push('--from', previousVersion);
     const handoffProbe = spawnSync(process.execPath, handoffArgs, {
         encoding: 'utf8', env: deps.env, cwd: deps.cwd,
-        stdio: ['ignore', 'pipe', 'pipe'], timeout: 30_000, killSignal: 'SIGKILL',
+        stdio: ['ignore', 'pipe', 'pipe'], timeout: 120_000, killSignal: 'SIGKILL',
     });
     let handoff = null;
     try {
         const value = JSON.parse(handoffProbe.stdout ?? '');
-        if (handoffProbe.status === 0 && typeof value === 'object' && value !== null &&
-            value.ok === true &&
-            value.read_only === true &&
-            value.running_version === effective.version) {
-            handoff = value;
+        if (typeof value === 'object' && value !== null) {
+            const record = value;
+            // Preserve structured partial progress from the new executable too.
+            // A successful package probe alone cannot prove integration finished.
+            if (record.read_only === false && record.running_version === effective.version &&
+                typeof record.files_complete === 'boolean' && record.ok === record.files_complete &&
+                handoffProbe.status === (record.files_complete ? EXIT.ok : EXIT.failed) &&
+                typeof record.migration_complete === 'boolean' && Array.isArray(record.pending_actions) &&
+                record.pending_actions.every(action => typeof action === 'string') &&
+                record.migration_complete === (record.files_complete && record.pending_actions.length === 0)) {
+                handoff = record;
+            }
         }
     }
     catch {
@@ -254,8 +266,10 @@ export function cliUpdateCommand(deps, requested) {
             update_prefix: targetPrefix,
             target: target ?? { version: null, dist_tag: 'latest' },
             handoff,
-            follow_up_required: true,
-            handoff_error: handoff === null ? 'Run notifai update --check --json with the updated CLI before claiming guidance or session readiness.' : null,
+            integration_complete: handoff?.migration_complete === true,
+            follow_up_required: handoff?.migration_complete !== true,
+            guidance_reread_required: true,
+            handoff_error: handoff === null ? 'Run notifai update --resume --json with the updated CLI to finish integration; update --check --json is read-only diagnosis.' : null,
             before,
             after,
             hook_adapter: adapterInspection === null
@@ -264,8 +278,8 @@ export function cliUpdateCommand(deps, requested) {
         }, null, 2));
     }
     else {
-        deps.io.out('The CLI is updated. Read the new release notes and guidance before continuing Notifai work.');
-        deps.io.out('Run `notifai update --check --json` for skill refresh and session requirements; a restart is not automatic.');
+        deps.io.out(handoff?.migration_complete === true ? 'The CLI and integration are verified. Read changed agent guidance.' : 'The package is installed; integration still needs follow-up. Run `notifai update --resume --json`.');
+        deps.io.out('Use `notifai update --check --json` for diagnosis; a restart is not automatic.');
     }
     return EXIT.ok;
 }

package/dist/commands-update.js.map

@@ -1 +1 @@
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package/dist/commands.d.ts

@@ -22,3 +22,4 @@ export { projectDisableCommand, projectEnableCommand, projectStatusCommand, } fr
 export { agentSessionRenameCommand } from './commands-agent-sessions.js';
 export { realIo } from './commands-io.js';
 export { updateSkillCommand } from './commands-update-skill.js';
+export { updateResumeCommand } from './commands-update-resume.js';

package/dist/commands.js

@@ -22,4 +22,5 @@ export { projectDisableCommand, projectEnableCommand, projectStatusCommand, } fr
 export { agentSessionRenameCommand } from './commands-agent-sessions.js';
 export { realIo } from './commands-io.js';
 export { updateSkillCommand } from './commands-update-skill.js';
+export { updateResumeCommand } from './commands-update-resume.js';
 //# sourceMappingURL=commands.js.map

package/dist/commands.js.map

@@ -1 +1 @@
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+{"version":3,"file":"commands.js","sourceRoot":"","sources":["../src/commands.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,IAAI,EACJ,gBAAgB,GAIjB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,mBAAmB,EACnB,iBAAiB,EACjB,YAAY,EACZ,aAAa,GACd,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,EACf,cAAc,GACf,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AACpD,OAAO,EACL,mBAAmB,EACnB,cAAc,EACd,WAAW,EACX,aAAa,GACd,MAAM,oBAAoB,CAAA;AAC3B,mFAAmF;AACnF,OAAO,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAA;AACzD,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAA;AAC9D,OAAO,EAAE,UAAU,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAA;AAChF,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAClD,OAAO,EACL,mBAAmB,EACnB,sCAAsC,EACtC,cAAc,GACf,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EAAE,mBAAmB,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAA;AACvF,OAAO,EACL,oBAAoB,EACpB,gBAAgB,EAChB,iBAAiB,EACjB,kBAAkB,GACnB,MAAM,sBAAsB,CAAA;AAC7B,OAAO,EACL,kBAAkB,EAClB,mBAAmB,EACnB,oBAAoB,GACrB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC5D,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AACnD,OAAO,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACjE,OAAO,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AACrE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAA;AAClE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAA;AACvD,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,oBAAoB,GACrB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,yBAAyB,EAAE,MAAM,8BAA8B,CAAA;AACxE,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAA;AAC/D,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA"}

package/dist/install-hooks.d.ts

@@ -337,17 +337,19 @@ export interface MergeResult {
     removed: string[];
 }
 /**
- * Adds our handlers without disturbing anyone else's. Re-running replaces only
- * the groups we previously wrote, so an upgrade that changes a timeout does not
- * accumulate duplicate hooks.
+ * Refresh owned handlers in their existing slots. Codex's approval identity
+ * includes group and handler indices, so stripping then appending an unchanged
+ * handler can revoke its approval and stale an active session's Stop definition.
+ * Missing handlers append after existing slots; foreign handlers and matcher
+ * metadata stay in place.
  *
- * Handlers are stripped from EVERY event, not just the ones being installed.
- * Only rewriting incoming events left a dropped event's handler in place for
- * ever, and since the binary no longer implements it, it exited 2 with
- * "Unknown hook event" every time the harness fired it — a permanent hook
- * failure that reinstalling could not clear.
+ * Retired handlers are considered in every event. Hosts without index-based
+ * approval can remove them; strict Codex repair refuses ambiguous removal so
+ * an explicit migration can account for native trust and active sessions.
  */
-export declare function mergeHooks(existing: SettingsDocument, incoming: HookConfig, scriptPath: string): MergeResult;
+export declare function mergeHooks(existing: SettingsDocument, incoming: HookConfig, scriptPath: string, options?: {
+    preserveIdentities?: boolean;
+}): MergeResult;
 export declare function removeHooks(existing: SettingsDocument, scriptPath: string): MergeResult;
 /**
  * Writes the settings file the way a tool that does not own it should.

package/dist/install-hooks.js

@@ -790,17 +790,17 @@ function withoutOurs(groups, scriptPath) {
     return { groups: kept, removed };
 }
 /**
- * Adds our handlers without disturbing anyone else's. Re-running replaces only
- * the groups we previously wrote, so an upgrade that changes a timeout does not
- * accumulate duplicate hooks.
+ * Refresh owned handlers in their existing slots. Codex's approval identity
+ * includes group and handler indices, so stripping then appending an unchanged
+ * handler can revoke its approval and stale an active session's Stop definition.
+ * Missing handlers append after existing slots; foreign handlers and matcher
+ * metadata stay in place.
  *
- * Handlers are stripped from EVERY event, not just the ones being installed.
- * Only rewriting incoming events left a dropped event's handler in place for
- * ever, and since the binary no longer implements it, it exited 2 with
- * "Unknown hook event" every time the harness fired it — a permanent hook
- * failure that reinstalling could not clear.
+ * Retired handlers are considered in every event. Hosts without index-based
+ * approval can remove them; strict Codex repair refuses ambiguous removal so
+ * an explicit migration can account for native trust and active sessions.
  */
-export function mergeHooks(existing, incoming, scriptPath) {
+export function mergeHooks(existing, incoming, scriptPath, options = {}) {
     const hooks = Object.create(null);
     const added = [];
     const replaced = [];
@@ -812,20 +812,54 @@ export function mergeHooks(existing, incoming, scriptPath) {
             hooks[event] = groups;
             continue;
         }
-        const { groups: foreign, removed: hadOurs } = withoutOurs(groups, scriptPath);
+        const desired = (incoming[event] ?? []).map(group => ({ ...group, hooks: [...group.hooks] }));
+        const refreshed = [];
+        let hadOurs = false;
+        for (const group of groups) {
+            const next = [];
+            for (const handler of group.hooks) {
+                if (!isOurHandler(handler, scriptPath)) {
+                    next.push(handler);
+                    continue;
+                }
+                hadOurs = true;
+                const replacementGroup = desired.find(candidate => candidate.hooks.some(replacement => handlerEvent(replacement.command) === handlerEvent(handler.command)));
+                const index = replacementGroup?.hooks.findIndex(replacement => handlerEvent(replacement.command) === handlerEvent(handler.command)) ?? -1;
+                if (replacementGroup !== undefined && index >= 0) {
+                    next.push(replacementGroup.hooks.splice(index, 1)[0]);
+                }
+                else if (options.preserveIdentities === true) {
+                    throw new Error(`Cannot preserve Codex hook identities for ${event}: duplicate or retired owned handlers require explicit migration. Review the existing hooks before retrying; the hook document was not changed.`);
+                }
+            }
+            // Empty native groups also occupy an approval index.
+            if (next.length > 0 || options.preserveIdentities === true)
+                refreshed.push({ ...group, hooks: next });
+        }
+        for (const group of desired.filter(candidate => candidate.hooks.length > 0)) {
+            // Append to a matching owned group without inserting before a foreign
+            // handler. An omitted matcher and '*' both cover the complete event.
+            const target = refreshed.find(candidate => (candidate.matcher ?? '*') === (group.matcher ?? '*') &&
+                candidate.hooks.some(handler => isOurHandler(handler, scriptPath)));
+            if (target === undefined)
+                refreshed.push(group);
+            else
+                target.hooks.push(...group.hooks);
+        }
         if (hadOurs) {
             if (event in incoming)
                 replaced.push(event);
             else
                 removed.push(event);
         }
-        if (foreign.length > 0)
-            hooks[event] = foreign;
+        if (refreshed.length > 0)
+            hooks[event] = refreshed;
     }
     for (const [event, groups] of Object.entries(incoming)) {
         if (!replaced.includes(event))
             added.push(event);
-        hooks[event] = [...(hooks[event] ?? []), ...groups];
+        if (!(event in (existing.hooks ?? {})))
+            hooks[event] = groups;
     }
     return { document: { ...existing, hooks }, added, replaced, removed };
 }