@agentteams/cli 0.1.78 → 0.1.81

package/dist/commands/attachment.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"attachment.d.ts","sourceRoot":"","sources":["../../src/commands/attachment.ts"],"names":[],"mappings":"AA+DA,wBAAsB,wBAAwB,CAC5C,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EAC/B,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC/B,OAAO,CAAC,OAAO,CAAC,CAoDlB"}
+{"version":3,"file":"attachment.d.ts","sourceRoot":"","sources":["../../src/commands/attachment.ts"],"names":[],"mappings":"AAmEA,wBAAsB,wBAAwB,CAC5C,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EAC/B,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC/B,OAAO,CAAC,OAAO,CAAC,CA8DlB"}

package/dist/commands/attachment.js

@@ -39,21 +39,35 @@ const resolveContentType = (fileName) => {
 const resolveTarget = (options) => {
     const codeReviewId = optionalString(options.codeReviewId);
     const completionReportId = optionalString(options.completionReportId);
-    if (codeReviewId && completionReportId) {
-        throw new Error('Use only one of --code-review-id or --completion-report-id.');
+    const documentId = optionalString(options.documentId);
+    const targets = [
+        codeReviewId ? { targetType: 'codeReview', targetId: codeReviewId } : null,
+        completionReportId ? { targetType: 'completionReport', targetId: completionReportId } : null,
+        documentId ? { targetType: 'document', targetId: documentId } : null,
+    ].filter((target) => target !== null);
+    if (targets.length > 1) {
+        throw new Error('Use only one of --code-review-id, --completion-report-id, or --document-id.');
     }
-    if (codeReviewId) {
-        return { targetType: 'codeReview', targetId: codeReviewId };
+    const target = targets[0];
+    if (target) {
+        return target;
     }
-    if (completionReportId) {
-        return { targetType: 'completionReport', targetId: completionReportId };
-    }
-    throw new Error('Exactly one of --code-review-id or --completion-report-id is required.');
+    throw new Error('Exactly one of --code-review-id, --completion-report-id, or --document-id is required.');
 };
 export async function executeAttachmentCommand(apiUrl, headers, action, options) {
     if (action === 'list') {
-        const triggerId = requireString(options.triggerId, '--trigger-id');
-        const response = await axios.get(`${apiUrl}/api/daemon-triggers/${triggerId}/attachments`, { headers });
+        const triggerId = optionalString(options.triggerId);
+        const documentId = optionalString(options.documentId);
+        if (triggerId && documentId) {
+            throw new Error('Use only one of --trigger-id or --document-id.');
+        }
+        if (!triggerId && !documentId) {
+            throw new Error('Exactly one of --trigger-id or --document-id is required.');
+        }
+        const path = documentId
+            ? `/api/documents/${documentId}/attachments`
+            : `/api/daemon-triggers/${triggerId}/attachments`;
+        const response = await axios.get(`${apiUrl}${path}`, { headers });
         return response.data;
     }
     if (action === 'create') {

package/dist/commands/attachment.js.map

@@ -1 +1 @@
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+{"version":3,"file":"attachment.js","sourceRoot":"","sources":["../../src/commands/attachment.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACnD,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAC9C,OAAO,KAAK,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AAExD,MAAM,aAAa,GAAG,CAAC,KAAc,EAAE,IAAY,EAAE,EAAE;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC3D,MAAM,IAAI,KAAK,CAAC,GAAG,IAAI,cAAc,CAAC,CAAC;IACzC,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,EAAE,CAAC;AACtB,CAAC,CAAC;AAEF,MAAM,cAAc,GAAG,CAAC,KAAc,EAAsB,EAAE;IAC5D,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACzD,OAAO,KAAK,CAAC,IAAI,EAAE,CAAC;IACtB,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC,CAAC;AAEF,MAAM,yBAAyB,GAA2B;IACxD,GAAG,EAAE,YAAY;IACjB,IAAI,EAAE,YAAY;IAClB,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,WAAW;IAChB,IAAI,EAAE,YAAY;IAClB,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,YAAY;IACjB,EAAE,EAAE,eAAe;IACnB,QAAQ,EAAE,eAAe;IACzB,GAAG,EAAE,iBAAiB;IACtB,IAAI,EAAE,WAAW;IACjB,GAAG,EAAE,WAAW;CACjB,CAAC;AAEF,MAAM,kBAAkB,GAAG,CAAC,QAAgB,EAAU,EAAE;IACtD,MAAM,GAAG,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IAC3F,MAAM,WAAW,GAAG,yBAAyB,CAAC,GAAG,CAAC,CAAC;IACnD,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,iCAAiC,GAAG,eAAe,MAAM,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACvG,CAAC;IACJ,CAAC;IACD,OAAO,WAAW,CAAC;AACrB,CAAC,CAAC;AAEF,MAAM,aAAa,GAAG,CACpB,OAAgC,EACkD,EAAE;IACpF,MAAM,YAAY,GAAG,cAAc,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;IAC1D,MAAM,kBAAkB,GAAG,cAAc,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAC;IACtE,MAAM,UAAU,GAAG,cAAc,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC;IACtD,MAAM,OAAO,GAAG;QACd,YAAY,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,YAAqB,EAAE,QAAQ,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC,IAAI;QACnF,kBAAkB,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,kBAA2B,EAAE,QAAQ,EAAE,kBAAkB,EAAE,CAAC,CAAC,CAAC,IAAI;QACrG,UAAU,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,UAAmB,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,IAAI;KAC9E,CAAC,MAAM,CAAC,CAAC,MAAM,EAAwC,EAAE,CAAC,MAAM,KAAK,IAAI,CAAC,CAAC;IAE5E,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,6EAA6E,CAAC,CAAC;IACjG,CAAC;IACD,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;IAC1B,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,MAAM,CAAC;IAChB,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,wFAAwF,CAAC,CAAC;AAC5G,CAAC,CAAC;AAEF,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAC5C,MAAc,EACd,OAA+B,EAC/B,MAAc,EACd,OAAgC;IAEhC,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,MAAM,SAAS,GAAG,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QACpD,MAAM,UAAU,GAAG,cAAc,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC;QACtD,IAAI,SAAS,IAAI,UAAU,EAAE,CAAC;YAC5B,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;QACpE,CAAC;QACD,IAAI,CAAC,SAAS,IAAI,CAAC,UAAU,EAAE,CAAC;YAC9B,MAAM,IAAI,KAAK,CAAC,2DAA2D,CAAC,CAAC;QAC/E,CAAC;QACD,MAAM,IAAI,GAAG,UAAU;YACrB,CAAC,CAAC,kBAAkB,UAAU,cAAc;YAC5C,CAAC,CAAC,wBAAwB,SAAS,cAAc,CAAC;QACpD,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,GAAG,MAAM,GAAG,IAAI,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC;QAClE,OAAO,QAAQ,CAAC,IAAI,CAAC;IACvB,CAAC;IAED,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QACxB,MAAM,cAAc,GAAG,aAAa,CAAC,OAAO,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;QAC7D,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,aAAa,CAAC,OAAO,CAAC,CAAC;QAExD,MAAM,QAAQ,GAAG,OAAO,CAAC,cAAc,CAAC,CAAC;QACzC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC1B,MAAM,IAAI,KAAK,CAAC,mBAAmB,cAAc,EAAE,CAAC,CAAC;QACvD,CAAC;QACD,MAAM,MAAM,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAC;QACtC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,2BAA2B,CAAC,CAAC;QAC/C,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;QACpC,MAAM,WAAW,GAAG,kBAAkB,CAAC,QAAQ,CAAC,CAAC;QACjD,iBAAiB,CAAC,cAAc,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;QAEjD,gCAAgC;QAChC,MAAM,aAAa,GAAG,MAAM,KAAK,CAAC,IAAI,CACpC,GAAG,MAAM,mCAAmC,EAC5C,EAAE,QAAQ,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,EAC9C,EAAE,OAAO,EAAE,CACZ,CAAC;QACF,MAAM,EAAE,SAAS,EAAE,GAAG,EAAE,GAAG,aAAa,CAAC,IAAI,CAAC,IAA0C,CAAC;QAEzF,yCAAyC;QACzC,MAAM,KAAK,CAAC,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,EAAE,cAAc,EAAE,WAAW,EAAE,EAAE,CAAC,CAAC;QAEjF,sBAAsB;QACtB,MAAM,cAAc,GAAG,MAAM,KAAK,CAAC,IAAI,CACrC,GAAG,MAAM,kBAAkB,EAC3B,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,YAAY,EAAE,QAAQ,EAAE,EACrD,EAAE,OAAO,EAAE,CACZ,CAAC;QACF,OAAO,cAAc,CAAC,IAAI,CAAC;IAC7B,CAAC;IAED,IAAI,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QAC/C,MAAM,IAAI,KAAK,CACb,eAAe,MAAM,iCAAiC;YACpD,sFAAsF,CACzF,CAAC;IACJ,CAAC;IAED,MAAM,IAAI,KAAK,CAAC,8BAA8B,MAAM,EAAE,CAAC,CAAC;AAC1D,CAAC"}

package/dist/commands/doctor.d.ts

@@ -1,5 +1,11 @@
 import { type ConventionIssue, type ConventionLinkState } from '../utils/conventionLink.js';
 export type DoctorStatus = 'READY' | 'DEGRADED' | 'NOT_APPLICABLE';
+/**
+ * Which project layout the diagnosis ran against. Output and readiness rules
+ * differ per layout, so this — not a derived field such as `rootHook` — is what
+ * consumers branch on.
+ */
+export type DoctorLayout = 'git-root' | 'non-git-root' | 'unknown';
 export interface DoctorIssue {
     code: string;
     path: string | null;
@@ -22,12 +28,20 @@ export interface DoctorRepositoryResult {
 }
 export interface DoctorResult {
     status: DoctorStatus;
+    layout: DoctorLayout;
     applicable: boolean;
     changedCount: number;
     rootDir: string | null;
     rootEntryPoints: string[];
     missingRecommendedEntryPoints: string[];
     repositories: DoctorRepositoryResult[];
+    /**
+     * State of the worktree bootstrap hook on the convention root itself. Only a
+     * git root project has one — a non-git root has no git-common dir and its
+     * hooks live per member repo (`DoctorRepositoryResult.hook`), so it reports
+     * `skipped`.
+     */
+    rootHook: 'ready' | 'blocked' | 'skipped';
     issues: DoctorIssue[];
 }
 type DoctorOptions = {

package/dist/commands/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAIA,OAAO,EAQL,KAAK,eAAe,EACpB,KAAK,mBAAmB,EACzB,MAAM,4BAA4B,CAAC;AAYpC,MAAM,MAAM,YAAY,GAAG,OAAO,GAAG,UAAU,GAAG,gBAAgB,CAAC;AAEnE,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,OAAO,GAAG,MAAM,CAAC;CAC5B;AAED,MAAM,WAAW,wBAAwB;IACvC,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,SAAS,GAAG,UAAU,CAAC;CAC/B;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,OAAO,GAAG,UAAU,CAAC;IAC7B,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,OAAO,GAAG,SAAS,CAAC;IAC7B,IAAI,EAAE,mBAAmB,CAAC;IAC1B,IAAI,EAAE,OAAO,GAAG,SAAS,GAAG,SAAS,CAAC;IACtC,mBAAmB,EAAE,wBAAwB,EAAE,CAAC;IAChD,MAAM,EAAE,eAAe,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,YAAY,CAAC;IACrB,UAAU,EAAE,OAAO,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,6BAA6B,EAAE,MAAM,EAAE,CAAC;IACxC,YAAY,EAAE,sBAAsB,EAAE,CAAC;IACvC,MAAM,EAAE,WAAW,EAAE,CAAC;CACvB;AAED,KAAK,aAAa,GAAG;IACnB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd,CAAC;AAqJF,wBAAsB,oBAAoB,CAAC,OAAO,CAAC,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAEzF"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAIA,OAAO,EAQL,KAAK,eAAe,EACpB,KAAK,mBAAmB,EACzB,MAAM,4BAA4B,CAAC;AAgBpC,MAAM,MAAM,YAAY,GAAG,OAAO,GAAG,UAAU,GAAG,gBAAgB,CAAC;AAEnE;;;;GAIG;AACH,MAAM,MAAM,YAAY,GAAG,UAAU,GAAG,cAAc,GAAG,SAAS,CAAC;AAEnE,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,OAAO,GAAG,MAAM,CAAC;CAC5B;AAED,MAAM,WAAW,wBAAwB;IACvC,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,SAAS,GAAG,UAAU,CAAC;CAC/B;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,OAAO,GAAG,UAAU,CAAC;IAC7B,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,OAAO,GAAG,SAAS,CAAC;IAC7B,IAAI,EAAE,mBAAmB,CAAC;IAC1B,IAAI,EAAE,OAAO,GAAG,SAAS,GAAG,SAAS,CAAC;IACtC,mBAAmB,EAAE,wBAAwB,EAAE,CAAC;IAChD,MAAM,EAAE,eAAe,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,YAAY,CAAC;IACrB,MAAM,EAAE,YAAY,CAAC;IACrB,UAAU,EAAE,OAAO,CAAC;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,6BAA6B,EAAE,MAAM,EAAE,CAAC;IACxC,YAAY,EAAE,sBAAsB,EAAE,CAAC;IACvC;;;;;OAKG;IACH,QAAQ,EAAE,OAAO,GAAG,SAAS,GAAG,SAAS,CAAC;IAC1C,MAAM,EAAE,WAAW,EAAE,CAAC;CACvB;AAED,KAAK,aAAa,GAAG;IACnB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd,CAAC;AAiNF,wBAAsB,oBAAoB,CAAC,OAAO,CAAC,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAEzF"}

package/dist/commands/doctor.js

@@ -11,6 +11,9 @@ const CONVENTION_FILE = 'convention.md';
 // which of these exist at the convention root; it never creates root files.
 const ENTRY_POINT_ALLOWLIST = ['CLAUDE.md', 'AGENTS.md', 'GEMINI.md', '.cursor/rules/agentteams.mdc'];
 const RECOMMENDED_ENTRY_POINTS = ['CLAUDE.md', 'AGENTS.md'];
+// Hook installation blocked by the user's own hook setup, not by a defect the
+// doctor can or should repair.
+const USER_HOOK_CONFIG_CODES = new Set(['hook-hookspath', 'hook-custom']);
 function pathEntryExists(path) {
     try {
         lstatSync(path);
@@ -23,15 +26,71 @@ function pathEntryExists(path) {
 function notApplicableResult(rootDir, issue) {
     return {
         status: 'NOT_APPLICABLE',
+        layout: 'unknown',
         applicable: false,
         changedCount: 0,
         rootDir,
         rootEntryPoints: [],
         missingRecommendedEntryPoints: [],
         repositories: [],
+        rootHook: 'skipped',
         issues: [issue],
     };
 }
+/**
+ * A git root project has no member repos to manage, but it does own the
+ * worktree bootstrap hook that makes `git worktree add` materialize
+ * conventions. That hook was previously reachable only from the interactive
+ * OAuth `init`, so any project configured before it existed had no way to get
+ * one. Installing it here is the doctor's whole job for this layout — member
+ * repo management (exclude, link, entry points) stays out of it.
+ *
+ * A project whose hook infrastructure the CLI must not touch is not a broken
+ * project: it keeps exit 0 (the code a git root project has always returned)
+ * and is told to use the manual per-worktree `agentteams init` fallback.
+ */
+function runGitRootDoctor(rootDir) {
+    const preflightIssues = validateRootPreflight(rootDir);
+    if (preflightIssues.length > 0) {
+        return {
+            status: 'DEGRADED',
+            layout: 'git-root',
+            applicable: true,
+            changedCount: 0,
+            rootDir,
+            rootEntryPoints: [],
+            missingRecommendedEntryPoints: [],
+            repositories: [],
+            rootHook: 'skipped',
+            issues: preflightIssues,
+        };
+    }
+    const hookResult = ensurePostCheckoutHook(rootDir);
+    const blockedByUserHookConfig = hookResult.status === 'blocked' && USER_HOOK_CONFIG_CODES.has(hookResult.issue?.code ?? '');
+    const issues = hookResult.issue
+        ? [
+            blockedByUserHookConfig
+                ? {
+                    ...hookResult.issue,
+                    message: `${hookResult.issue.message} Run 'agentteams init' from the root of each new worktree instead.`,
+                    severity: 'info',
+                }
+                : { ...hookResult.issue, severity: 'error' },
+        ]
+        : [];
+    return {
+        status: hookResult.status === 'ready' || blockedByUserHookConfig ? 'READY' : 'DEGRADED',
+        layout: 'git-root',
+        applicable: true,
+        changedCount: hookResult.changed ? 1 : 0,
+        rootDir,
+        rootEntryPoints: [],
+        missingRecommendedEntryPoints: [],
+        repositories: [],
+        rootHook: hookResult.status,
+        issues,
+    };
+}
 /**
  * Validate the root before any member mutation. The check never echoes the
  * config body or API key — only paths appear in issues.
@@ -176,24 +235,21 @@ function runDoctor(options) {
         });
     }
     if (!isNonGitRootProject(rootDir)) {
-        return notApplicableResult(rootDir, {
-            code: 'git-root-project',
-            path: rootDir,
-            message: `${rootDir} is a git repository root project; the doctor only manages non-git root projects.`,
-            severity: 'info',
-        });
+        return runGitRootDoctor(rootDir);
     }
     const issues = [];
     const preflightIssues = validateRootPreflight(rootDir);
     if (preflightIssues.length > 0) {
         return {
             status: 'DEGRADED',
+            layout: 'non-git-root',
             applicable: true,
             changedCount: 0,
             rootDir,
             rootEntryPoints: [],
             missingRecommendedEntryPoints: [],
             repositories: [],
+            rootHook: 'skipped',
             issues: preflightIssues,
         };
     }
@@ -234,12 +290,15 @@ function runDoctor(options) {
     const degraded = issues.some((issue) => issue.severity === 'error') || repositories.some((repo) => repo.status === 'DEGRADED');
     return {
         status: degraded ? 'DEGRADED' : 'READY',
+        layout: 'non-git-root',
         applicable: true,
         changedCount: repositories.reduce((sum, repo) => sum + repo.changedCount, 0),
         rootDir,
         rootEntryPoints: [...rootEntryPoints],
         missingRecommendedEntryPoints: [...missingRecommendedEntryPoints],
         repositories,
+        // Hooks for this layout are installed per member repo, not on the root.
+        rootHook: 'skipped',
         issues,
     };
 }

package/dist/commands/doctor.js.map

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package/dist/commands/init.d.ts

@@ -30,7 +30,7 @@ export type WorktreeInitResult = {
     worktreePath: string;
     sourcePath: string;
     targetPath: string;
-    materialization: 'symlink' | 'copy' | 'existing' | 'blocked';
+    materialization: 'symlink' | 'copy' | 'relinked' | 'existing' | 'blocked';
     entryPoints: WorktreeEntryPointEntry[];
     issues: ConventionIssue[];
     warning?: string;

package/dist/commands/init.d.ts.map

@@ -1 +1 @@
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package/dist/commands/init.js

@@ -1,4 +1,4 @@
-import { appendFileSync, cpSync, existsSync, lstatSync, mkdirSync, readFileSync, realpathSync, symlinkSync, unlinkSync, writeFileSync, } from 'node:fs';
+import { appendFileSync, cpSync, existsSync, lstatSync, mkdirSync, readFileSync, readdirSync, realpathSync, renameSync, rmSync, statSync, symlinkSync, unlinkSync, writeFileSync, } from 'node:fs';
 import { basename, dirname, join, resolve } from 'node:path';
 import { constants, createCipheriv, publicEncrypt, randomBytes } from 'node:crypto';
 import { multiselect, isCancel, cancel } from '@clack/prompts';
@@ -11,7 +11,7 @@ import { withCommandContext } from '../utils/commandContext.js';
 import { conventionDownload } from './convention.js';
 import { resolveGitTopLevel, resolveMainCheckoutRoot } from '../utils/git.js';
 import { buildAuthHeaders } from '../utils/apiContext.js';
-import { DEFAULT_CONVENTION_REFERENCE, ensureConventionEntryPoints, ensureLocalExclude, ensurePostCheckoutHook, isReadableRegularFile, toAnchoredExcludePattern, } from '../utils/conventionLink.js';
+import { DEFAULT_CONVENTION_REFERENCE, ensureConventionEntryPoints, ensureLocalExclude, ensurePostCheckoutHook, isReadableRegularFile, resolveGitCommonDir, toAnchoredExcludePattern, } from '../utils/conventionLink.js';
 const AUTH_BASE_URL = process.env.AGENTTEAMS_WEB_URL || 'https://agentteams.run';
 const AGENT_ENTRY_POINT_FILES = [
     { value: 'CLAUDE.md', label: 'CLAUDE.md', hint: 'Claude Code' },
@@ -22,6 +22,7 @@ const AGENT_ENTRY_POINT_FILES = [
 const CONFIG_DIR = '.agentteams';
 const CONFIG_FILE = 'config.json';
 const CONVENTION_FILE = 'convention.md';
+const RELINK_BACKUP_NAME = 'agentteams-relink';
 const AUTH_PATH_PUBLIC_KEY_PEM = `-----BEGIN PUBLIC KEY-----
 MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAs9s9+n0C8Z099LrOTlKB
 83c2WluO/TxZFxJQ07XgfKJ2RG/8K2kvCwVKeSgzzBP/hmY2qWAgAOrXIoSHNYGt
@@ -232,6 +233,221 @@ function isConfiguredMainCheckout(sourcePath) {
         return false;
     }
 }
+/**
+ * Materialize the worktree's `.agentteams` entry as a real link.
+ *
+ * Windows directory symlinks require SeCreateSymbolicLinkPrivilege (Developer
+ * Mode or elevation), so an unprivileged win32 run fails with EPERM and used to
+ * fall through to a copy — silently breaking the guarantee that a worktree
+ * tracks the main checkout's conventions. Junctions need no privilege, which is
+ * why `utils/conventionLink.ts` and the daemon's worktree helper already use
+ * them; this is the same documented platform exception.
+ *
+ * The copy fallback stays for environments neither link type supports (UNC
+ * paths, filesystems without reparse points). It dereferences because in a
+ * non-git-root layout the source is itself a link, and copying a link
+ * recursively re-creates it — which fails for exactly the same reason.
+ */
+function linkConventionDir(sourcePath, targetPath) {
+    try {
+        if (process.platform === 'win32') {
+            // Junctions only accept absolute targets, so resolve the chain first.
+            symlinkSync(realpathSync(sourcePath), targetPath, 'junction');
+        }
+        else {
+            symlinkSync(sourcePath, targetPath, 'dir');
+        }
+        return { materialization: 'symlink' };
+    }
+    catch (error) {
+        cpSync(sourcePath, targetPath, { recursive: true, dereference: true });
+        return {
+            materialization: 'copy',
+            warning: `Could not create the .agentteams symlink (${error instanceof Error ? error.message : String(error)}). Copied the directory instead.`,
+        };
+    }
+}
+/**
+ * Decide whether a plain directory sitting at the worktree's `.agentteams` may
+ * be the copy an earlier failed link attempt left behind, rather than something
+ * the user created. Identity is judged by the config file, the one artifact a
+ * copy reproduces byte for byte — anything else is treated as the user's and is
+ * never touched. This only authorizes moving the directory aside; whether the
+ * moved copy may be deleted is decided separately by `findCopyOnlyFiles`.
+ */
+function isCopyOfMainCheckout(sourcePath, targetPath) {
+    try {
+        return (readFileSync(join(targetPath, CONFIG_FILE), 'utf-8') === readFileSync(join(sourcePath, CONFIG_FILE), 'utf-8'));
+    }
+    catch {
+        return false;
+    }
+}
+function toErrorMessage(error) {
+    return error instanceof Error ? error.message : String(error);
+}
+function hasIdenticalFile(sourceFile, backupFile) {
+    try {
+        const sourceStats = statSync(sourceFile);
+        if (!sourceStats.isFile() || sourceStats.size !== statSync(backupFile).size)
+            return false;
+        return readFileSync(sourceFile).equals(readFileSync(backupFile));
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * List every file in the moved-aside copy that the main checkout does not
+ * already hold byte for byte. A worktree that ran as a copy accumulates its own
+ * artifacts inside `.agentteams` — runner history, evidence, downloaded plans,
+ * review findings — and none of them can be regenerated, so the copy is only
+ * safe to delete when it is a strict subset of the source. Anything that is not
+ * a plain matching file (a symlink, a special file, an unreadable directory)
+ * counts as copy-only: it cannot be proven redundant.
+ */
+function findCopyOnlyFiles(backupPath, sourcePath) {
+    const copyOnlyFiles = [];
+    const walk = (relativeDir) => {
+        let entries;
+        try {
+            entries = readdirSync(join(backupPath, relativeDir), { withFileTypes: true });
+        }
+        catch {
+            copyOnlyFiles.push(relativeDir || '.');
+            return;
+        }
+        for (const entry of entries) {
+            const relativePath = relativeDir ? join(relativeDir, entry.name) : entry.name;
+            if (entry.isDirectory()) {
+                walk(relativePath);
+            }
+            else if (!entry.isFile() || !hasIdenticalFile(join(sourcePath, relativePath), join(backupPath, relativePath))) {
+                copyOnlyFiles.push(relativePath);
+            }
+        }
+    };
+    walk('');
+    return copyOnlyFiles;
+}
+/**
+ * Park the copy outside every tracked surface while the link is created. A
+ * backup next to `.agentteams` would show up in `git status` — the anchored
+ * `/.agentteams` exclude is an exact match and does not cover a sibling name —
+ * and the copied `config.json` carries the project apiKey. `git-common-dir` is
+ * part of no working tree, so nothing can surface from there. A worktree on a
+ * different volume cannot be renamed into it, and only then does the
+ * in-worktree fallback apply — after registering its own exclude pattern.
+ */
+function moveConventionCopyAside(worktreePath, targetPath) {
+    const failures = [];
+    const commonDir = resolveGitCommonDir(worktreePath);
+    if (commonDir) {
+        const backupPath = join(commonDir, `${RELINK_BACKUP_NAME}-${process.pid}`);
+        try {
+            renameSync(targetPath, backupPath);
+            return { backupPath };
+        }
+        catch (error) {
+            failures.push(toErrorMessage(error));
+        }
+    }
+    const excludeResult = ensureLocalExclude(worktreePath, [toAnchoredExcludePattern(`.${RELINK_BACKUP_NAME}`)]);
+    if (excludeResult.status !== 'ready') {
+        failures.push(`the in-worktree backup cannot be kept out of git status (${excludeResult.issue?.message ?? 'local exclude is blocked'})`);
+        return { error: failures.join('; ') };
+    }
+    try {
+        const backupPath = join(worktreePath, `.${RELINK_BACKUP_NAME}`);
+        renameSync(targetPath, backupPath);
+        return { backupPath };
+    }
+    catch (error) {
+        failures.push(toErrorMessage(error));
+        return { error: failures.join('; ') };
+    }
+}
+/** Undo the move-aside. The target may hold a fresh link or a partial copy, and
+ * `renameSync` onto a non-empty directory fails with ENOTEMPTY, so clear it
+ * first and never let the restore itself escape as an exception. */
+function restoreConventionCopy(backupPath, targetPath) {
+    try {
+        rmSync(targetPath, { recursive: true, force: true });
+        renameSync(backupPath, targetPath);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Replace a copied `.agentteams` directory with a real link so a worktree that
+ * predates the link fix starts tracking the main checkout again. Without this
+ * the `existing` branch treats the copy as settled and the worktree keeps
+ * serving stale conventions forever.
+ *
+ * The copy is moved aside first and is deleted only once the link is in place
+ * *and* the copy proves to be a strict subset of the main checkout; otherwise
+ * the backup is kept and its path reported. Any failure restores the original
+ * directory, and a failed restore reports where the original is.
+ */
+function promoteCopiedConventionDir(worktreePath, sourcePath, targetPath) {
+    if (!isCopyOfMainCheckout(sourcePath, targetPath)) {
+        return {
+            materialization: 'existing',
+            issue: {
+                code: 'link-occupied',
+                path: targetPath,
+                message: `The directory at ${targetPath} does not match the main checkout's ${CONFIG_DIR}; leaving it untouched. Remove it manually to restore the convention link.`,
+            },
+        };
+    }
+    const moved = moveConventionCopyAside(worktreePath, targetPath);
+    if ('error' in moved) {
+        return {
+            materialization: 'existing',
+            issue: {
+                code: 'link-create-failed',
+                path: targetPath,
+                message: `Could not move the copied ${CONFIG_DIR} aside at ${targetPath}: ${moved.error}`,
+            },
+        };
+    }
+    const { backupPath } = moved;
+    try {
+        const { materialization } = linkConventionDir(sourcePath, targetPath);
+        // A copy fallback here would only rebuild the state being replaced.
+        if (materialization !== 'symlink') {
+            throw new Error('the link could not be created and a copy would not restore the convention chain');
+        }
+    }
+    catch (error) {
+        const restored = restoreConventionCopy(backupPath, targetPath);
+        return {
+            materialization: 'existing',
+            issue: {
+                code: 'link-create-failed',
+                path: targetPath,
+                message: restored
+                    ? `Could not relink ${targetPath} to the main checkout: ${toErrorMessage(error)}`
+                    : `Could not relink ${targetPath} to the main checkout: ${toErrorMessage(error)}. The original ${CONFIG_DIR} was left at ${backupPath}; move it back manually.`,
+            },
+        };
+    }
+    const copyOnlyFiles = findCopyOnlyFiles(backupPath, sourcePath);
+    if (copyOnlyFiles.length > 0) {
+        return {
+            materialization: 'relinked',
+            issue: {
+                code: 'link-backup-retained',
+                path: backupPath,
+                message: `Kept ${copyOnlyFiles.length} file(s) that exist only in the replaced ${CONFIG_DIR} copy (${copyOnlyFiles.slice(0, 3).join(', ')}${copyOnlyFiles.length > 3 ? ', …' : ''}) at ${backupPath}; move what you still need out of it and delete it.`,
+            },
+        };
+    }
+    rmSync(backupPath, { recursive: true, force: true });
+    return { materialization: 'relinked' };
+}
 function isBrokenSymbolicLink(path) {
     try {
         return lstatSync(path).isSymbolicLink() && !existsSync(path);
@@ -289,30 +505,25 @@ export function bootstrapLinkedWorktree(cwd) {
     }
     else if (isBrokenSymbolicLink(targetPath)) {
         unlinkSync(targetPath);
-        try {
-            symlinkSync(sourcePath, targetPath, 'dir');
-            materialization = 'symlink';
-        }
-        catch (error) {
-            warning = `Could not create the .agentteams symlink (${error instanceof Error ? error.message : String(error)}). Copied the directory instead.`;
-            cpSync(sourcePath, targetPath, { recursive: true });
-            materialization = 'copy';
-        }
+        ({ materialization, warning } = linkConventionDir(sourcePath, targetPath));
     }
     else if (existsSync(targetPath)) {
-        materialization = 'existing';
-    }
-    else {
-        try {
-            symlinkSync(sourcePath, targetPath, 'dir');
-            materialization = 'symlink';
+        // An entry that is already a link is settled; a plain directory is either a
+        // copy left by a failed link attempt or something the user put there.
+        if (lstatSync(targetPath).isSymbolicLink()) {
+            materialization = 'existing';
         }
-        catch (error) {
-            warning = `Could not create the .agentteams symlink (${error instanceof Error ? error.message : String(error)}). Copied the directory instead.`;
-            cpSync(sourcePath, targetPath, { recursive: true });
-            materialization = 'copy';
+        else {
+            const promotion = promoteCopiedConventionDir(worktreePath, sourcePath, targetPath);
+            materialization = promotion.materialization;
+            if (promotion.issue) {
+                issues.push(promotion.issue);
+            }
         }
     }
+    else {
+        ({ materialization, warning } = linkConventionDir(sourcePath, targetPath));
+    }
     const entryPointResult = ensureConventionEntryPoints(worktreePath, selectedEntryPoints, {
         allowCreate: excludeReady,
         validateExistingReference: false,