@cleocode/core 2026.9.19 → 2026.9.21

package/dist/doctor/project-identity.js

@@ -19,16 +19,40 @@
  * The tracked file is never modified here. It is write-once, and a malformed
  * one is restored from version control, never regenerated.
  *
+ * T12557: `projectRoot` is a path fact, derived from the real root at runtime.
+ * A persisted copy in `project-info.json` or `project-context.json` goes stale
+ * on every move, so the inspection lists it under `derivedFields` and
+ * `--resolve` strips it. Each removed value is kept in `project-info.json`
+ * under `strippedFields`, the same in-file receipt pattern as
+ * `previousProjectIds`. `projectHash` is NOT a path fact: it is a write-once
+ * identity key, and nothing here ever touches it.
+ *
  * @task T12353
+ * @task T12557
  * @see ADR-094 — write-once portable project identity (amends ADR-013 §9)
  */
 import { execFileSync } from 'node:child_process';
 import { existsSync, readFileSync, renameSync, writeFileSync } from 'node:fs';
 import { join } from 'node:path';
-import { getCleoHome, isValidPortableProjectId, PORTABLE_PROJECT_ID_FILE, readPortableProjectId, } from '@cleocode/paths';
+import { canonicalizePath, getCleoHome, isValidPortableProjectId, PORTABLE_PROJECT_ID_FILE, readDeclaredProjectIdentity, readPortableProjectId, } from '@cleocode/paths';
 import { ensurePortableProjectId } from '../scaffold/project-identity.js';
+import { detectRelocatedRoot } from '../store/relocated-store-guard.js';
 /** Command that reports identity state; the prefix of every remedy below. */
 const IDENTITY_COMMAND = 'cleo doctor project-identity';
+/** Files that must not persist path-derived fields. */
+const DERIVED_FIELD_FILES = [
+    'project-info.json',
+    'project-context.json',
+];
+/**
+ * Path facts derived from the real root at runtime, never authoritative on
+ * disk. `projectHash` is deliberately absent: it is a write-once identity key.
+ */
+const DERIVED_FIELDS = ['projectRoot'];
+/** Schema `maxItems` for the `previousProjectIds` / `strippedFields` receipts; oldest drop first. */
+const RECEIPT_MAX_ITEMS = 50;
+/** Bound every git probe: briefing runs this inspection on each call. */
+const GIT_PROBE_TIMEOUT_MS = 5000;
 /** Read the id and the whole object from `project-info.json`; `undefined` when absent. */
 function readInfo(projectRoot) {
     const path = join(projectRoot, '.cleo', 'project-info.json');
@@ -43,12 +67,40 @@ function readInfo(projectRoot) {
         return 'unparseable';
     }
 }
+/** Read a `.cleo/` JSON object; `undefined` when absent or not an object. */
+function readCleoJson(projectRoot, file) {
+    const path = join(projectRoot, '.cleo', file);
+    if (!existsSync(path))
+        return undefined;
+    try {
+        const data = JSON.parse(readFileSync(path, 'utf-8'));
+        return data !== null && typeof data === 'object' && !Array.isArray(data)
+            ? data
+            : undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
+/** List persisted path-derived fields across the metadata files (T12557). */
+function findDerivedFields(projectRoot) {
+    const found = [];
+    for (const file of DERIVED_FIELD_FILES) {
+        const data = readCleoJson(projectRoot, file);
+        if (!data)
+            continue;
+        for (const field of DERIVED_FIELDS)
+            if (field in data)
+                found.push({ file, field, value: data[field] });
+    }
+    return found;
+}
 /** Git's view of the tracked file: `null` when this is not a git work tree. */
 function gitFileState(projectRoot) {
     const rel = `.cleo/${PORTABLE_PROJECT_ID_FILE}`;
     const run = (args) => {
         try {
-            execFileSync('git', args, { cwd: projectRoot, stdio: 'pipe' });
+            execFileSync('git', args, { cwd: projectRoot, stdio: 'pipe', timeout: GIT_PROBE_TIMEOUT_MS });
             return true;
         }
         catch {
@@ -80,16 +132,37 @@ export function inspectProjectIdentity(projectRoot) {
     const info = readInfo(projectRoot);
     const trackedId = tracked.status === 'valid' ? tracked.projectId : null;
     const localId = info && info !== 'unparseable' ? info.id : null;
-    const base = { projectRoot, trackedId, localId };
+    const base = { projectRoot, trackedId, localId, derivedFields: findDerivedFields(projectRoot) };
+    // A CLEO root need not be a git work tree; git remedies apply only inside one.
+    let git;
+    const gitState = () => {
+        if (git === undefined)
+            git = gitFileState(projectRoot);
+        return git;
+    };
     if (tracked.status === 'invalid') {
         return {
             ...base,
             state: 'invalid',
             message: `.cleo/project-id is unusable (${tracked.reason}). CLEO never regenerates it.`,
-            remedy: 'git checkout -- .cleo/project-id   (restore the committed id; inspect with `git log -p -- .cleo/project-id`)',
+            remedy: gitState() === null
+                ? 'restore .cleo/project-id from a backup of this project (the CLEO root is not a git work tree)'
+                : 'git checkout -- .cleo/project-id   (restore the committed id; inspect with `git log -p -- .cleo/project-id`)',
         };
     }
     if (info === undefined) {
+        // T12558: a tracked id restored (e.g. by `git checkout -- .`) at a root the
+        // project was rerooted away from must not be "adopted" by a plain init —
+        // that is exactly the refusal. Point at the live root, or the opt-out.
+        const relocated = detectRelocatedRoot(projectRoot, join(getCleoHome(), 'cleo.db'));
+        if (relocated) {
+            return {
+                ...base,
+                state: 'not-adopted',
+                message: `.cleo/project-id declares ${relocated.projectId}, which was rerooted from here to ${relocated.movedTo} (${relocated.via}).`,
+                remedy: `cd "${relocated.movedTo}"   (the live project). A DIFFERENT project here needs a new id: \`cleo init --here --new-identity\``,
+            };
+        }
         return trackedId
             ? {
                 ...base,
@@ -117,7 +190,9 @@ export function inspectProjectIdentity(projectRoot) {
             ...base,
             state: 'missing',
             message: `.cleo/project-id is missing. The local id is ${localId}.`,
-            remedy: `${IDENTITY_COMMAND} --resolve && git add .cleo/project-id && git commit -m "chore: track CLEO project id"`,
+            remedy: gitState() === null
+                ? `${IDENTITY_COMMAND} --resolve   (the CLEO root is not a git work tree; keep .cleo/project-id with the project)`
+                : `${IDENTITY_COMMAND} --resolve && git add .cleo/project-id && git commit -m "chore: track CLEO project id"`,
         };
     }
     if (trackedId !== localId) {
@@ -128,8 +203,7 @@ export function inspectProjectIdentity(projectRoot) {
             remedy: `${IDENTITY_COMMAND} --resolve --dry-run   then   ${IDENTITY_COMMAND} --resolve   (re-keys local state to ${trackedId}; ${localId} stays resolvable as an alias)`,
         };
     }
-    const git = gitFileState(projectRoot);
-    if (git === 'ignored') {
+    if (gitState() === 'ignored') {
         return {
             ...base,
             state: 'ignored',
@@ -137,7 +211,7 @@ export function inspectProjectIdentity(projectRoot) {
             remedy: 'cleo upgrade   (refreshes .cleo/.gitignore with `!project-id`), then git add .cleo/project-id',
         };
     }
-    if (git === 'untracked') {
+    if (gitState() === 'untracked') {
         return {
             ...base,
             state: 'untracked',
@@ -158,6 +232,120 @@ function writeJsonAtomic(path, data) {
     writeFileSync(tmp, `${JSON.stringify(data, null, 2)}\n`);
     renameSync(tmp, path);
 }
+/** Whether git tracks `.cleo/<file>`, so rewriting it dirties the work tree. */
+function isGitTracked(projectRoot, file) {
+    try {
+        execFileSync('git', ['ls-files', '--error-unmatch', `.cleo/${file}`], {
+            cwd: projectRoot,
+            stdio: 'pipe',
+            timeout: GIT_PROBE_TIMEOUT_MS,
+        });
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Return `info` with `findings` appended to its `strippedFields` receipt
+ * (capped at the schema's `maxItems`) and, when `stripInfo`, its own path
+ * facts removed. Pure; the caller writes the result.
+ *
+ * @param info - Parsed `project-info.json`.
+ * @param findings - Path facts being removed, with their values.
+ * @param now - ISO timestamp recorded on each receipt entry.
+ * @param stripInfo - Remove `DERIVED_FIELDS` from `info` itself.
+ * @returns A new object; `info` is not mutated.
+ * @example
+ * ```ts
+ * const next = withStrippedFieldsReceipt(info, findings, new Date().toISOString(), true);
+ * ```
+ * @task T12557
+ */
+export function withStrippedFieldsReceipt(info, findings, now, stripInfo) {
+    const next = { ...info };
+    const prior = Array.isArray(info['strippedFields']) ? info['strippedFields'] : [];
+    next['strippedFields'] = [
+        ...prior,
+        ...findings.map((finding) => ({ ...finding, strippedAt: now })),
+    ].slice(-RECEIPT_MAX_ITEMS);
+    if (stripInfo)
+        for (const field of DERIVED_FIELDS)
+            delete next[field];
+    return next;
+}
+/**
+ * Remove persisted path facts. The receipt is written first, into
+ * `project-info.json` `strippedFields`, so a value is never removed without a
+ * durable record of it; without a readable `project-info.json` nothing is
+ * stripped.
+ */
+function stripDerivedFields(projectRoot, findings, now) {
+    const info = readCleoJson(projectRoot, 'project-info.json');
+    if (!info)
+        return false;
+    const stripInfo = findings.some((finding) => finding.file === 'project-info.json');
+    writeJsonAtomic(join(projectRoot, '.cleo', 'project-info.json'), withStrippedFieldsReceipt(info, findings, now, stripInfo));
+    if (findings.some((finding) => finding.file === 'project-context.json')) {
+        const context = readCleoJson(projectRoot, 'project-context.json');
+        if (context) {
+            for (const field of DERIVED_FIELDS)
+                delete context[field];
+            writeJsonAtomic(join(projectRoot, '.cleo', 'project-context.json'), context);
+        }
+    }
+    return true;
+}
+/**
+ * Find this checkout's `candidate` location: it declares an id whose registry
+ * row names another path, and it is not already a live location on this device.
+ */
+async function findCandidateCheckout(projectRoot, cleoHome) {
+    const declared = readDeclaredProjectIdentity(projectRoot);
+    if (!declared)
+        return null;
+    const path = canonicalizePath(projectRoot);
+    const { getNexusRegistryDb } = await import('../store/nexus-sqlite.js');
+    const { projectRegistry } = await import('../store/schema/nexus-schema.js');
+    const { eq } = await import('drizzle-orm');
+    const { decideEncounterBinding } = await import('../nexus/path-map.js');
+    const db = await getNexusRegistryDb(cleoHome ?? getCleoHome());
+    const row = db
+        .select({ projectPath: projectRegistry.projectPath })
+        .from(projectRegistry)
+        .where(eq(projectRegistry.projectId, declared.projectId))
+        .get();
+    if (!row || row.projectPath === path)
+        return null;
+    const binding = decideEncounterBinding(db, {
+        projectId: declared.projectId,
+        projectPath: path,
+        now: new Date().toISOString(),
+    });
+    if (binding === 'refresh')
+        return null;
+    return { projectId: declared.projectId, path, registeredPath: row.projectPath };
+}
+/** Promote a candidate checkout to the project's live, registered location. */
+async function confirmCandidateCheckout(candidate, cleoHome) {
+    const { getNexusRegistryDb } = await import('../store/nexus-sqlite.js');
+    const { confirmProjectLocation } = await import('../nexus/path-map.js');
+    const { collectCheckoutEvidence } = await import('../nexus/identity.js');
+    const { ensureCheckoutNonce } = await import('../nexus/checkout-nonce.js');
+    const evidence = await collectCheckoutEvidence(candidate.path);
+    // The confirmed checkout gets its own nonce, so a later move is provable.
+    const checkoutNonce = ensureCheckoutNonce(candidate.path);
+    const db = await getNexusRegistryDb(cleoHome ?? getCleoHome());
+    db.transaction((tx) => {
+        confirmProjectLocation(tx, {
+            projectId: candidate.projectId,
+            projectPath: candidate.path,
+            now: new Date().toISOString(),
+            evidence,
+            checkoutNonce,
+        });
+    }, { behavior: 'immediate' });
+}
 /**
  * Resolve the identity state that {@link inspectProjectIdentity} reported.
  *
@@ -167,6 +355,9 @@ function writeJsonAtomic(path, data) {
  *   renames the row's primary key, re-points aliases and records the old id as
  *   an alias. Then `project-info.json` is rewritten, keeping the old id under
  *   `previousProjectIds`.
+ * - In every state, persisted `projectRoot` fields are stripped first
+ *   (T12557). The removed values are kept in `project-info.json`
+ *   `strippedFields`. `projectHash` is never touched.
  *
  * Every other state is refused with its remedy. The operation is idempotent:
  * re-running after a partial apply completes the remaining steps.
@@ -186,6 +377,36 @@ export async function resolveProjectIdentity(projectRoot, options = {}) {
     const before = inspectProjectIdentity(projectRoot);
     const steps = [];
     const result = (refused, rows = { before: 0, after: 0 }) => ({ dryRun, before, steps, registryRows: rows, refused });
+    // T12470: a checkout that declares an already-registered id is only a
+    // `candidate` until confirmed. Resolving here IS the explicit confirmation.
+    const confirmCandidateStep = async () => {
+        const candidate = await findCandidateCheckout(projectRoot, options.cleoHome);
+        if (!candidate)
+            return false;
+        steps.push({
+            action: 'confirm-candidate-location',
+            detail: `confirm ${candidate.path} as the live location of ${candidate.projectId} (registry row moves from ${candidate.registeredPath}; its permissions stay with the row)`,
+        });
+        if (!dryRun)
+            await confirmCandidateCheckout(candidate, options.cleoHome);
+        return true;
+    };
+    if (before.derivedFields.length > 0) {
+        const removed = before.derivedFields
+            .map((finding) => `${finding.file}:${finding.field}=${JSON.stringify(finding.value)}`)
+            .join(', ');
+        const trackedNote = before.derivedFields.some((finding) => finding.file === 'project-context.json')
+            ? isGitTracked(projectRoot, 'project-context.json')
+                ? '; .cleo/project-context.json is git-tracked, so this dirties the work tree (commit the change)'
+                : '; .cleo/project-context.json is not git-tracked'
+            : '';
+        steps.push({
+            action: 'strip-derived-fields',
+            detail: `remove ${removed} (a path fact derived at runtime; a persisted copy goes stale on a move). Receipt: project-info.json strippedFields${trackedNote}`,
+        });
+        if (!dryRun && !stripDerivedFields(projectRoot, before.derivedFields, new Date().toISOString()))
+            return result('Cannot record a strip receipt: .cleo/project-info.json is missing or unreadable.');
+    }
     if (before.state === 'missing' && before.localId) {
         steps.push({
             action: 'write-tracked-id',
@@ -193,6 +414,7 @@ export async function resolveProjectIdentity(projectRoot, options = {}) {
         });
         if (!dryRun)
             await ensurePortableProjectId(projectRoot, before.localId);
+        await confirmCandidateStep();
         return result(null);
     }
     if (before.state === 'info-invalid') {
@@ -204,10 +426,15 @@ export async function resolveProjectIdentity(projectRoot, options = {}) {
             const { ensureProjectInfo } = await import('../scaffold/ensure-config.js');
             await ensureProjectInfo(projectRoot, { force: true });
         }
+        await confirmCandidateStep();
         return result(null);
     }
+    if (before.state !== 'conflict' && (await confirmCandidateStep()))
+        return result(null);
     if (before.state !== 'conflict' || !before.trackedId || !before.localId) {
-        return result(before.remedy ? `${before.message} Remedy: ${before.remedy}` : 'Nothing to resolve.');
+        if (before.remedy)
+            return result(`${before.message} Remedy: ${before.remedy}`);
+        return result(steps.length > 0 ? null : 'Nothing to resolve.');
     }
     const oldId = before.localId;
     const newId = before.trackedId;
@@ -298,7 +525,7 @@ export async function resolveProjectIdentity(projectRoot, options = {}) {
         writeJsonAtomic(join(projectRoot, '.cleo', 'project-info.json'), {
             ...info.data,
             projectId: newId,
-            previousProjectIds: [...new Set([...previous, oldId])],
+            previousProjectIds: [...new Set([...previous, oldId])].slice(-RECEIPT_MAX_ITEMS),
             lastUpdated: now,
         });
     }

package/dist/doctor/project-identity.js.map

@@ -1 +1 @@
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package/dist/doctor/projects.d.ts

@@ -0,0 +1,170 @@
+/**
+ * `cleo doctor projects` — machine-wide integrity check of the project
+ * registry (T12471 · ADR-094).
+ *
+ * The registry is keyed by project id, never by path. A path is a per-device
+ * hint that goes stale when a project moves, is deleted, or is re-initialized
+ * under a new id. This module walks every registry row, probes its path, scans
+ * the directories projects live in for `.cleo/` declarations, and classifies
+ * each row (see `NexusRegistryFindingKind`):
+ *
+ * - {@link inspectProjectRegistry} is read-only and returns every non-`ok`
+ *   row with its exact remedy.
+ * - {@link applyProjectRegistryRepair} applies only the safe classes: a
+ *   `moved` row is rebound to the one path that declares its id, a
+ *   `missing` row's location is recorded as `missing`, and an alias row whose
+ *   truncated legacy key several projects claim is removed (T12589). No
+ *   registry row is deleted. The rows the changes touch are imaged before and
+ *   after, and both images are written to `nexus_audit_log` in the same
+ *   transaction as the changes.
+ * - {@link rollbackProjectRegistryRepair} restores the before image, guarded
+ *   on the current rows still matching the after image.
+ *
+ * Split identities, ambiguous moves, temp rows and home/root rows are owner
+ * decisions: they are reported with a remedy and never changed.
+ *
+ * Probes are bounded: at most `concurrency` filesystem reads at once, each
+ * with a `timeoutMs` budget. Only ENOENT/ENOTDIR prove a path gone; EACCES,
+ * EPERM or a timeout leave the row `unreadable` and untouched (#1606).
+ *
+ * @task T12471
+ * @epic T12468
+ * @see ADR-094 — write-once portable project identity
+ */
+import type { NexusRegistryIntegrityReport, NexusRegistryRollbackResult } from '@cleocode/contracts';
+/** Options shared by inspect and apply. */
+export interface ProjectRegistryScanOptions {
+    /** Extra directories to scan for `.cleo/`, beyond the registry-derived parents. */
+    roots?: readonly string[];
+    /** Scan depth below each root (default 2). */
+    maxDepth?: number;
+    /** Filesystem reads in flight at once (default 16). */
+    concurrency?: number;
+    /** Budget per filesystem probe in milliseconds (default 2000). */
+    timeoutMs?: number;
+    /** Global CLEO home whose registry is checked (defaults to the current one). */
+    cleoHome?: string;
+}
+/** Error with a stable code, raised when a rollback is refused. */
+export declare class RegistryRepairError extends Error {
+    readonly code: 'E_NOT_FOUND' | 'E_ROLLBACK_CONFLICT';
+    /** @override */
+    readonly name = "RegistryRepairError";
+    /**
+     * @param code - Stable error code (`E_NOT_FOUND`, `E_ROLLBACK_CONFLICT`).
+     * @param message - Explanation with the remedy.
+     */
+    constructor(code: 'E_NOT_FOUND' | 'E_ROLLBACK_CONFLICT', message: string);
+}
+/**
+ * Whether a registry path is a temp row: under a temp directory while the
+ * registry itself is persistent. A sandboxed registry (temp `CLEO_HOME`) keeps
+ * its temp fixtures legitimately, as encounter registration does.
+ *
+ * @param projectPath - Registered path.
+ * @param cleoHome - Home of the registry being checked.
+ * @returns `true` for a temp row.
+ *
+ * @example
+ * ```ts
+ * isTempRegistryPath('/tmp/fixture', '/home/me/.local/share/cleo'); // true
+ * ```
+ */
+export declare function isTempRegistryPath(projectPath: string, cleoHome: string): boolean;
+/**
+ * Whether a registry path is the home directory or a filesystem root: a
+ * project registered there claims every directory below it.
+ *
+ * @param projectPath - Registered path.
+ * @param home - Home directory (defaults to the current user's).
+ * @returns `true` for a home or root row.
+ *
+ * @example
+ * ```ts
+ * isHomeOrRootPath('/'); // true
+ * ```
+ */
+export declare function isHomeOrRootPath(projectPath: string, home?: string): boolean;
+/**
+ * Whether `path` lies in a trash directory. A project the owner trashed is
+ * never a move target, and its registry row may be cleaned.
+ *
+ * @param path - Absolute path.
+ * @returns `true` inside `.Trash`, `.Trashes`, `$RECYCLE.BIN` or `.local/share/Trash`.
+ *
+ * @example
+ * ```ts
+ * isTrashPath('/Users/me/.Trash/app'); // true
+ * ```
+ */
+export declare function isTrashPath(path: string): boolean;
+/**
+ * Classify every registry row, read-only.
+ *
+ * @param opts - Extra scan roots, depth, concurrency, per-probe budget, registry home.
+ * @returns Counts per kind and every non-`ok` row with its exact remedy.
+ *
+ * @example
+ * ```ts
+ * const report = await inspectProjectRegistry({ roots: ['/home/me/src'] });
+ * for (const f of report.findings) console.log(f.kind, f.projectPath, f.remedy);
+ * ```
+ */
+export declare function inspectProjectRegistry(opts?: ProjectRegistryScanOptions): Promise<NexusRegistryIntegrityReport>;
+/**
+ * Inspect, then apply the safe repairs: rebind every `moved` row to the path
+ * that declares its id, record every `missing` row's location as
+ * `missing`, and remove every alias row whose key several projects claim
+ * (T12589). One immediate transaction makes the changes and writes the
+ * receipt (before and after images of every touched row, alias rows
+ * included) to `nexus_audit_log`. No registry row is deleted, and nothing
+ * outside the registry is written. A row that changed since inspection is
+ * skipped.
+ *
+ * @param opts - Same options as {@link inspectProjectRegistry}.
+ * @returns The report, with `dryRun: false` and a receipt when anything applied.
+ *
+ * @example
+ * ```ts
+ * const result = await applyProjectRegistryRepair();
+ * if (result.receipt) console.log(result.receipt.rollback);
+ * ```
+ */
+export declare function applyProjectRegistryRepair(opts?: ProjectRegistryScanOptions): Promise<NexusRegistryIntegrityReport>;
+/**
+ * Restore the rows an applied repair changed. Refused when the receipt is
+ * unknown, was already rolled back, or when any row in its scope changed
+ * since the repair (the current rows must equal the receipt's after image) —
+ * a later edit is never overwritten. The rollback writes its own receipt.
+ *
+ * @param receiptId - `receiptId` from {@link applyProjectRegistryRepair}.
+ * @param opts - Registry home.
+ * @returns Rows restored per table and the rollback's own receipt id.
+ * @throws RegistryRepairError (`E_NOT_FOUND`, `E_ROLLBACK_CONFLICT`).
+ *
+ * @example
+ * ```ts
+ * await rollbackProjectRegistryRepair(receipt.receiptId);
+ * ```
+ */
+export declare function rollbackProjectRegistryRepair(receiptId: string, opts?: Pick<ProjectRegistryScanOptions, 'cleoHome'>): Promise<NexusRegistryRollbackResult>;
+/**
+ * For each id, the paths on this device other than `exclude` that provably
+ * hold it now: recorded locations of the id that still declare it, plus
+ * directories found by scanning `roots`. Used by `nexus projects clean` to
+ * refuse deleting a row whose project merely moved (T12471).
+ *
+ * @param ids - Project ids to look for, with the registered path to exclude.
+ * @param opts - Scan roots and budgets; roots default to the parents of the given paths.
+ * @returns Map from id to the paths that declare it (ids found nowhere are absent).
+ *
+ * @example
+ * ```ts
+ * const found = await locateProjectsElsewhere([{ projectId, projectPath }]);
+ * ```
+ */
+export declare function locateProjectsElsewhere(ids: ReadonlyArray<{
+    projectId: string;
+    projectPath: string;
+}>, opts?: ProjectRegistryScanOptions): Promise<Map<string, string[]>>;
+//# sourceMappingURL=projects.d.ts.map

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

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