@cleocode/core 2026.9.19 → 2026.9.21

package/dist/orchestration/spawn.d.ts

@@ -65,6 +65,13 @@ export interface ComposeSpawnPayloadOptions {
     role?: AgentSpawnCapability;
     /** Harness hint override. Default: {@link resolveHarnessHint}. */
     harnessHint?: HarnessHint;
+    /**
+     * CAAMP provider id of the orchestrator's harness, used to name its ask
+     * tool in the subagent's HITL line. Default: derived from `harnessHint`.
+     *
+     * @task T12482
+     */
+    askProviderId?: string;
     /** Project root for path + profile resolution. Default: `process.cwd()`. */
     projectRoot?: string;
     /**

package/dist/orchestration/spawn.d.ts.map

@@ -1 +1 @@
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package/dist/orchestration/spawn.js

@@ -376,6 +376,7 @@ export async function composeSpawnPayload(db, task, options = {}) {
         projectRoot,
         sessionId: options.sessionId ?? null,
         harnessHint,
+        ...(options.askProviderId !== undefined ? { askProviderId: options.askProviderId } : {}),
         skipCleoInjectionEmbed: !shouldEmbedInjection,
         worktreePath: options.worktreePath,
         worktreeBranch: options.worktreeBranch,

package/dist/orchestration/spawn.js.map

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

@@ -15,7 +15,7 @@
  * @task T4458
  */
 export type { WorktreeScope } from './project-scope.js';
-export { getProjectRoot, validateProjectRoot, worktreeScope } from './project-scope.js';
+export { getProjectRoot, isGitLinkedCheckout, linkedWorktreeMainRoot, resolveStoreOwnerRoot, validateProjectRoot, worktreeScope, } from './project-scope.js';
 /**
  * Run `fn` inside a `worktreeScope.run()` AsyncLocalStorage frame derived
  * from the `CLEO_WORKTREE_ROOT` and `CLEO_PROJECT_HASH` environment variables.
@@ -252,25 +252,34 @@ export declare function getCleoDirAbsolute(cwd?: string, opts?: {
  */
 export declare function resolveCanonicalCleoDir(projectId: string): string;
 /**
- * Resolve the canonical projectId from a working directory.
+ * Resolve the project id from a working directory.
  *
- * First reads `.cleo/project-info.json` from CWD or an ancestor directory (AC2).
- * Falls back to nexus registry `project_registry.project_path` match when no
- * local `project-info.json` is found (AC3).
+ * Resolution order (T12470 · ADR-094) — the id is always DECLARED, never
+ * derived from a path:
+ *   1. An absolute `CLEO_DIR` pin: the pinned root's declared id.
+ *   2. The nearest ancestor (or, from a git worktree, its main checkout) whose
+ *      `.cleo/` declares an id: tracked `.cleo/project-id`, then
+ *      `project-info.json`.
+ *   3. The registry's recorded location for this directory — a suggestion used
+ *      only when no ancestor declares an identity.
+ *
+ * Old path-derived ids handed in by callers keep resolving through
+ * `nexus_project_id_aliases` in `resolveCanonicalCleoDir`.
  *
  * @param cwd - Optional working directory. Defaults to `process.cwd()`.
- * @returns The canonical projectId string (AC4).
+ * @returns The opaque project id.
  * @throws {CleoError} `ExitCode.NEXUS_PROJECT_NOT_FOUND` (E_CLEO_NEXUS_PROJECT_NOT_FOUND)
- *   with a remediation hint when no CLEO project is found (AC5).
+ *   with a remediation hint when no CLEO project is found.
  *
  * @example
  * ```typescript
  * const projectId = resolveProjectByCwd('/repo/packages/core');
- * // "a1b2c3d4e5f6"
+ * // "c78d09c3a8ee" — the content of /repo/.cleo/project-id
  * ```
  *
  * @public
  * @task T11013
+ * @task T12470
  */
 export declare function resolveProjectByCwd(cwd?: string): string;
 /**
@@ -290,6 +299,13 @@ export declare function resolveProjectByCwd(cwd?: string): string;
  *   3. Nearest ancestor containing a `.cleo/` directory — presence of `.cleo/`
  *      identifies the project root (`<root>/.cleo`); no `project-info.json` or
  *      nexus registration required. Bounded by the `$HOME`/`/` guard.
+ *
+ *   Steps 1 and 3 map their root through {@link resolveStoreOwnerRoot}: a CLEO
+ *   worktree (a linked git checkout whose parent is a CLEO project) resolves to
+ *   the PARENT project's `.cleo/`, even when the worktree carries its own
+ *   `.cleo/` (tracked files, or the seeded `project-info.json`). Without this a
+ *   worktree opened an empty local `cleo.db`, auto-recovered a full copy of the
+ *   parent's newest snapshot into it, and every write there was lost (T12460).
  *   4. Cross-project nexus `project_registry` lookup by `cwd` — for callers
  *      whose `cwd` is not under a `.cleo/` tree but is registered.
  *   5. Throw `E_NO_PROJECT` with a remediation hint.

package/dist/paths.d.ts.map

@@ -1 +1 @@
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package/dist/paths.js

@@ -19,11 +19,11 @@ import { createRequire } from 'node:module';
 import { homedir } from 'node:os';
 import { basename, dirname, join, resolve } from 'node:path';
 import { E_CWD_WALKUP_FORBIDDEN, ExitCode } from '@cleocode/contracts';
-import { computeCanonicalProjectId as _computeCanonicalProjectId, getCanonicalTemplatesTildePath as _getCanonicalTemplatesTildePath, getCleoTemplatesTildePath as _getCleoTemplatesTildePath, isAbsolutePath as _isAbsolutePath, resolveProjectByCwd as _pathsResolveProjectByCwd, resolveCanonicalCleoDir as _resolveCanonicalCleoDir, } from '@cleocode/paths';
+import { getCanonicalTemplatesTildePath as _getCanonicalTemplatesTildePath, getCleoTemplatesTildePath as _getCleoTemplatesTildePath, isAbsolutePath as _isAbsolutePath, resolveProjectByCwd as _pathsResolveProjectByCwd, readDeclaredProjectIdentity as _readDeclaredProjectIdentity, resolveCanonicalCleoDir as _resolveCanonicalCleoDir, } from '@cleocode/paths';
 import { CleoError } from './errors.js';
 import { registryStorePath, shouldAutoRegisterProject } from './nexus/registry-hygiene.js';
-import { _resolveMainRepoFromGitlink, captureProjectScope, getProjectRoot, validateProjectRoot, worktreeScope, } from './project-scope.js';
-export { getProjectRoot, validateProjectRoot, worktreeScope } from './project-scope.js';
+import { _resolveMainRepoFromGitlink, captureProjectScope, getProjectRoot, resolveStoreOwnerRoot, validateProjectRoot, worktreeScope, } from './project-scope.js';
+export { getProjectRoot, isGitLinkedCheckout, linkedWorktreeMainRoot, resolveStoreOwnerRoot, validateProjectRoot, worktreeScope, } from './project-scope.js';
 import { createOperationExecutionContext, isExpectedTeardownRejection, trackBackgroundOp, } from './store/background-ops.js';
 import { getPlatformPaths } from './system/platform-paths.js';
 import { isShuttingDown } from './teardown-signal.js';
@@ -334,15 +334,14 @@ export function getCleoDirAbsolute(cwd, opts) {
     const project = _pathsResolveProjectByCwd(cwd);
     if (project !== null) {
         // T11021: Schedule lifecycle-tracked registration against captured global ownership.
-        // T11023: pass legacyUUID so it gets registered as an alias alongside
-        // the canonical ID.
+        // T12470: the declared id (tracked `.cleo/project-id` first) owns the row.
         // T11281: unit tests that exercise the nexus registration/reconcile contract
         // in isolation set CLEO_DISABLE_PROJECT_AUTOREGISTER=1 so this encounter-time
         // side-effect does not pre-register the fixture project out from under the
         // test's explicit registration state. Off by default — production always
         // auto-registers on encounter.
         if (process.env['CLEO_DISABLE_PROJECT_AUTOREGISTER'] !== '1') {
-            scheduleProjectEncounter(project.projectRoot, project.legacyUUID ?? project.projectId);
+            scheduleProjectEncounter(project.projectRoot, project.projectId);
         }
         try {
             const projectRoot = getProjectRoot(cwd);
@@ -546,50 +545,63 @@ function _findCleoDirRoot(cwd) {
     return null;
 }
 /**
- * Resolve the canonical projectId from a working directory.
+ * Resolve the project id from a working directory.
  *
- * First reads `.cleo/project-info.json` from CWD or an ancestor directory (AC2).
- * Falls back to nexus registry `project_registry.project_path` match when no
- * local `project-info.json` is found (AC3).
+ * Resolution order (T12470 · ADR-094) — the id is always DECLARED, never
+ * derived from a path:
+ *   1. An absolute `CLEO_DIR` pin: the pinned root's declared id.
+ *   2. The nearest ancestor (or, from a git worktree, its main checkout) whose
+ *      `.cleo/` declares an id: tracked `.cleo/project-id`, then
+ *      `project-info.json`.
+ *   3. The registry's recorded location for this directory — a suggestion used
+ *      only when no ancestor declares an identity.
+ *
+ * Old path-derived ids handed in by callers keep resolving through
+ * `nexus_project_id_aliases` in `resolveCanonicalCleoDir`.
  *
  * @param cwd - Optional working directory. Defaults to `process.cwd()`.
- * @returns The canonical projectId string (AC4).
+ * @returns The opaque project id.
  * @throws {CleoError} `ExitCode.NEXUS_PROJECT_NOT_FOUND` (E_CLEO_NEXUS_PROJECT_NOT_FOUND)
- *   with a remediation hint when no CLEO project is found (AC5).
+ *   with a remediation hint when no CLEO project is found.
  *
  * @example
  * ```typescript
  * const projectId = resolveProjectByCwd('/repo/packages/core');
- * // "a1b2c3d4e5f6"
+ * // "c78d09c3a8ee" — the content of /repo/.cleo/project-id
  * ```
  *
  * @public
  * @task T11013
+ * @task T12470
  */
 export function resolveProjectByCwd(cwd) {
-    // CLEO_DIR override (backward-compat, T11262 regression fix). When CLEO_DIR
-    // is an absolute path it pins the project for the whole process; return a
-    // deterministic projectId derived from the pinned project root so callers
-    // that chain into resolveCanonicalCleoDir (which also honours CLEO_DIR) never
-    // hit the empty-registry NEXUS_PROJECT_NOT_FOUND throw. See _cleoDirEnvOverride.
+    let from = cwd;
+    // CLEO_DIR override (backward-compat, T11262). An absolute CLEO_DIR pins the
+    // project for the whole process. T12470: return the pinned root's DECLARED
+    // id — never a hash of its path. A pinned root that declares nothing is
+    // resolved by the ordinary chain FROM THAT ROOT, never from the process cwd
+    // (which may sit inside a different project).
     const overrideDir = _cleoDirEnvOverride();
     if (overrideDir !== null) {
         const projectRoot = overrideDir.replace(/[\\/]\.cleo$/, '');
-        return _computeCanonicalProjectId(projectRoot);
+        const declared = _readDeclaredProjectIdentity(projectRoot);
+        if (declared !== null)
+            return declared.projectId;
+        from = projectRoot;
     }
-    // AC2: Try local project-info.json first (via paths package)
-    const pathsResult = _pathsResolveProjectByCwd(cwd);
+    // Declared identity: tracked .cleo/project-id, then project-info.json.
+    const pathsResult = _pathsResolveProjectByCwd(from);
     if (pathsResult !== null) {
         return pathsResult.projectId;
     }
     // AC4: Walk up from cwd looking for git worktree gitlinks.
     // When cwd is inside a worktree (`.git` is a FILE pointing to main repo),
-    // resolve the main repo and try project-info.json there.
+    // resolve the main repo and read its declared identity there.
     // This handles the canonical CLEO worktree layout where worktrees live
     // under ~/.local/share/cleo/worktrees/<hash>/<taskId>/ — completely
     // separate from the main repo — and therefore ancestor-walk from cwd
-    // will never encounter the main repo's .cleo/project-info.json.
-    const start = resolve(cwd ?? process.cwd());
+    // will never encounter the main repo's `.cleo/`.
+    const start = resolve(from ?? process.cwd());
     let current = start;
     while (true) {
         const mainRepo = _resolveMainRepoFromGitlink(current);
@@ -598,7 +610,7 @@ export function resolveProjectByCwd(cwd) {
             if (mainRepoResult !== null) {
                 return mainRepoResult.projectId;
             }
-            // Found a gitlink but the main repo has no project-info.json —
+            // Found a gitlink but the main repo declares no identity —
             // don't keep walking up past the gitlink; the worktree's ancestors
             // won't help.
             break;
@@ -608,8 +620,8 @@ export function resolveProjectByCwd(cwd) {
             break;
         current = parent;
     }
-    // AC3: Fall back to nexus registry lookup
-    const nexusProjectId = _resolveProjectByCwdFromNexus(cwd);
+    // Suggestion only: the registry's recorded location for this directory.
+    const nexusProjectId = _resolveProjectByCwdFromNexus(from);
     if (nexusProjectId !== null) {
         return nexusProjectId;
     }
@@ -636,6 +648,13 @@ export function resolveProjectByCwd(cwd) {
  *   3. Nearest ancestor containing a `.cleo/` directory — presence of `.cleo/`
  *      identifies the project root (`<root>/.cleo`); no `project-info.json` or
  *      nexus registration required. Bounded by the `$HOME`/`/` guard.
+ *
+ *   Steps 1 and 3 map their root through {@link resolveStoreOwnerRoot}: a CLEO
+ *   worktree (a linked git checkout whose parent is a CLEO project) resolves to
+ *   the PARENT project's `.cleo/`, even when the worktree carries its own
+ *   `.cleo/` (tracked files, or the seeded `project-info.json`). Without this a
+ *   worktree opened an empty local `cleo.db`, auto-recovered a full copy of the
+ *   parent's newest snapshot into it, and every write there was lost (T12460).
  *   4. Cross-project nexus `project_registry` lookup by `cwd` — for callers
  *      whose `cwd` is not under a `.cleo/` tree but is registered.
  *   5. Throw `E_NO_PROJECT` with a remediation hint.
@@ -651,7 +670,7 @@ export function resolveCleoDir(cwd) {
     // 1. Active worktree scope wins (matches getProjectRoot precedence).
     const scope = worktreeScope.getStore();
     if (scope !== undefined) {
-        return join(scope.worktreeRoot, '.cleo');
+        return join(resolveStoreOwnerRoot(scope.worktreeRoot), '.cleo');
     }
     // 2. Absolute CLEO_DIR override.
     const override = _cleoDirEnvOverride();
@@ -659,9 +678,10 @@ export function resolveCleoDir(cwd) {
         return override;
     }
     // 3. Nearest ancestor with a `.cleo/` directory — presence = project root.
+    //    A worktree's own `.cleo/` never owns the store (T12460).
     const root = _findCleoDirRoot(cwd);
     if (root !== null) {
-        return join(root, '.cleo');
+        return join(resolveStoreOwnerRoot(root), '.cleo');
     }
     // 3b. Worktree gitlink: when `cwd` is inside a git worktree (`.git` is a FILE
     //     pointing to `<mainRepo>/.git/worktrees/<name>`), the canonical project
@@ -1661,7 +1681,7 @@ export async function resolveProjectById(projectId) {
         if (!existsSync(getNexusRegistryDbPath()))
             return null;
         const { eq } = await import('drizzle-orm');
-        const { projectRegistry, projectIdAliases } = await import('./store/schema/nexus-schema.js');
+        const { projectRegistry } = await import('./store/schema/nexus-schema.js');
         const db = await getNexusDb();
         const directRows = await db
             .select()
@@ -1670,15 +1690,13 @@ export async function resolveProjectById(projectId) {
             .limit(1);
         if (directRows.length > 0)
             return _rowToRegistryEntry(directRows[0]);
-        // Alias lookup (AC4) — gracefully handles missing project_id_aliases table
+        // Alias lookup (AC4) — gracefully handles missing project_id_aliases table.
+        // T12589: an alias shared by several projects resolves to none of them.
         try {
-            const aliasRows = await db
-                .select()
-                .from(projectIdAliases)
-                .where(eq(projectIdAliases.legacyId, projectId))
-                .limit(1);
-            if (aliasRows.length > 0) {
-                const canonicalId = aliasRows[0].canonicalId;
+            const { resolveProjectAlias } = await import('./nexus/legacy-alias.js');
+            const alias = resolveProjectAlias(db, projectId);
+            if (alias.status === 'resolved') {
+                const canonicalId = alias.canonicalId;
                 const canonicalRows = await db
                     .select()
                     .from(projectRegistry)
@@ -1829,27 +1847,30 @@ export async function recordProjectEncounter(cwd) {
     const project = _pathsResolveProjectByCwd(start);
     if (project === null)
         return 'no-project';
-    const infoProjectId = project.legacyUUID ?? project.projectId;
+    const infoProjectId = project.projectId;
     const cleoHome = getCleoHome();
     if (!shouldAutoRegisterProject(project.projectRoot, cleoHome))
         return 'ephemeral';
     const checkout = captureProjectScope(project.projectRoot, worktreeScope.getStore()).worktreeRoot;
     const { getNexusRegistryDb, getNexusRegistryDbPath } = await import('./store/nexus-sqlite.js');
     if (existsSync(getNexusRegistryDbPath(cleoHome))) {
-        const { eq } = await import('drizzle-orm');
-        const { projectPaths, projectRegistry } = await import('./store/schema/nexus-schema.js');
+        const { and, eq } = await import('drizzle-orm');
+        const { projectLocations, projectRegistry } = await import('./store/schema/nexus-schema.js');
+        const { currentDeviceId } = await import('./nexus/path-map.js');
         const db = await getNexusRegistryDb(cleoHome);
         const row = db
             .select({ projectPath: projectRegistry.projectPath })
             .from(projectRegistry)
             .where(eq(projectRegistry.projectId, infoProjectId))
             .get();
-        const mapped = db
-            .select({ projectId: projectPaths.projectId })
-            .from(projectPaths)
-            .where(eq(projectPaths.projectPath, checkout))
+        // T12469: current only when this checkout is a LIVE location of this id
+        // on this device; the unique holder of a path is never assumed.
+        const located = db
+            .select({ state: projectLocations.state })
+            .from(projectLocations)
+            .where(and(eq(projectLocations.projectId, infoProjectId), eq(projectLocations.deviceId, currentDeviceId()), eq(projectLocations.path, checkout)))
             .get();
-        if (row?.projectPath === checkout && mapped?.projectId === infoProjectId)
+        if (row?.projectPath === checkout && located?.state === 'live')
             return 'current';
     }
     const key = `${cleoHome}\u0000${infoProjectId}\u0000${project.projectRoot}`;
@@ -1888,32 +1909,70 @@ export async function registerProjectOnEncounter(projectRoot, infoProjectId) {
         });
     try {
         const outcome = await trackBackgroundOp(() => worktreeScope.run({ ...scope, execution }, async () => {
-            const { canonicalProjectId, legacyProjectId } = await import('./nexus/identity.js');
+            const { collectCheckoutEvidence, projectPathFingerprint, legacyProjectId } = await import('./nexus/identity.js');
+            const { ensureCheckoutNonce, readCheckoutNonce } = await import('./nexus/checkout-nonce.js');
             const { generateProjectHash } = await import('./nexus/hash.js');
-            const canonical = await canonicalProjectId(resolvedPath, execution);
+            // Path-derived values are ALIASES of the declared id, never the id (T12470).
+            const canonical = await projectPathFingerprint(resolvedPath, execution);
+            const evidence = await collectCheckoutEvidence(resolvedPath, execution);
             execution.assertActive();
             const { getNexusRegistryDb } = await import('./store/nexus-sqlite.js');
-            const { eq, or } = await import('drizzle-orm');
+            const { eq } = await import('drizzle-orm');
             const { projectRegistry, projectIdAliases } = await import('./store/schema/nexus-schema.js');
-            const { recordProjectCheckout } = await import('./nexus/path-map.js');
+            const { decideEncounterBinding, recordCandidateLocation, recordProjectCheckout, touchProjectLocation, } = await import('./nexus/path-map.js');
+            const { registryAliasClaimants } = await import('./nexus/legacy-alias.js');
             const db = await getNexusRegistryDb(capturedHome);
             execution.assertActive();
             const projectHash = generateProjectHash(resolvedPath);
             const legacyAlias = legacyProjectId(resolvedPath);
             const skippedAliases = [];
+            let candidateOf = null;
             const aliases = new Set([legacyAlias, canonical.id, ...(canonical.legacyAliases ?? [])]);
             aliases.delete(infoProjectId);
             db.transaction((tx) => {
                 execution.assertActive();
-                const owners = tx
+                const now = new Date().toISOString();
+                const unconfirmed = {
+                    projectId: infoProjectId,
+                    projectPath: resolvedPath,
+                    projectHash,
+                    now,
+                    evidence,
+                    checkoutNonce: readCheckoutNonce(resolvedPath),
+                };
+                // T12470: an encounter runs under ANY command, read-only ones
+                // included, and the id it sees is committed to git — any
+                // directory can declare it. It never repoints an existing row
+                // to a new path (nor hands that row's permissions over) unless
+                // the move is PROVEN by this checkout's untracked nonce;
+                // otherwise the path is only a candidate.
+                const binding = decideEncounterBinding(tx, unconfirmed);
+                if (binding === 'candidate') {
+                    if (!recordCandidateLocation(tx, unconfirmed))
+                        return;
+                    const holder = tx
+                        .select({ projectPath: projectRegistry.projectPath })
+                        .from(projectRegistry)
+                        .where(eq(projectRegistry.projectId, infoProjectId))
+                        .get();
+                    candidateOf = holder?.projectPath ?? null;
+                    return;
+                }
+                // Confirmed: make sure the checkout carries a nonce, so a later
+                // move of it can be proven.
+                const record = {
+                    ...unconfirmed,
+                    checkoutNonce: unconfirmed.checkoutNonce ?? ensureCheckoutNonce(resolvedPath),
+                };
+                if (binding === 'refresh') {
+                    touchProjectLocation(tx, record);
+                    return;
+                }
+                const existing = tx
                     .select()
                     .from(projectRegistry)
-                    .where(or(eq(projectRegistry.projectId, infoProjectId), eq(projectRegistry.projectPath, resolvedPath), eq(projectRegistry.projectHash, projectHash)))
-                    .all();
-                if (owners.some((owner) => owner.projectId !== infoProjectId))
-                    throw new Error('Project encounter path or hash belongs to another immutable identity');
-                const now = new Date().toISOString();
-                const existing = owners.find((owner) => owner.projectId === infoProjectId);
+                    .where(eq(projectRegistry.projectId, infoProjectId))
+                    .get();
                 if (existing) {
                     tx.update(projectRegistry)
                         .set({
@@ -1947,19 +2006,21 @@ export async function registerProjectOnEncounter(projectRoot, infoProjectId) {
                     })
                         .run();
                 }
-                // T12354: every checkout is recorded; the row above names the latest.
-                recordProjectCheckout(tx, {
-                    projectId: infoProjectId,
-                    projectPath: resolvedPath,
-                    projectHash,
-                    now,
-                });
+                // T12354 · T12469: every confirmed checkout is a live location.
+                recordProjectCheckout(tx, record);
                 for (const alias of aliases) {
                     const owner = tx
                         .select()
                         .from(projectIdAliases)
                         .where(eq(projectIdAliases.legacyId, alias))
                         .get();
+                    // T12589: the legacy key encodes only 24 path bytes, so every
+                    // project under a shared prefix derives it. Shared, it names no
+                    // project: never recorded for a second one and never resolved
+                    // (legacy-alias.ts). Expected, so not reported.
+                    if (alias === legacyAlias &&
+                        registryAliasClaimants(tx, alias, owner?.canonicalId).some((id) => id !== infoProjectId))
+                        continue;
                     const directOwner = tx
                         .select()
                         .from(projectRegistry)
@@ -1967,13 +2028,12 @@ export async function registerProjectOnEncounter(projectRoot, infoProjectId) {
                         .get();
                     if ((owner && owner.canonicalId !== infoProjectId) ||
                         (directOwner && directOwner.projectId !== infoProjectId)) {
-                        // Match explicit registration: this old truncated token is lossy.
-                        // Preserve its existing owner; the immutable identity still registers.
-                        if (alias === legacyAlias) {
-                            skippedAliases.push(alias);
-                            continue;
-                        }
-                        throw new Error('Project encounter alias belongs to another immutable identity');
+                        // Every alias here is derived from the PATH (base64url path,
+                        // git-root hash), so another project owning it means the path
+                        // changed hands — not a conflict of identity (T12469). Keep the
+                        // existing owner; the immutable identity still registers.
+                        skippedAliases.push(alias);
+                        continue;
                     }
                     if (!owner)
                         tx.insert(projectIdAliases)
@@ -1984,6 +2044,10 @@ export async function registerProjectOnEncounter(projectRoot, infoProjectId) {
             }, { behavior: 'immediate' });
             if (skippedAliases.length > 0)
                 process.stderr.write(`[cleo] Project encounter omitted colliding legacy alias: ${skippedAliases.join(', ')}\n`);
+            if (candidateOf !== null)
+                process.stderr.write(`[cleo] ${resolvedPath} declares project ${infoProjectId}, which is registered at ${candidateOf}; ` +
+                    'recorded as an unconfirmed candidate location (nothing proves it is the same checkout). ' +
+                    'If it is, confirm with `cleo doctor project-identity --resolve`.\n');
         }), execution);
         if (outcome.status === 'rejected')
             throw outcome.reason;