@askdkc/kiokuko 0.1.28 → 0.1.30

package/dist/commands/doctor.js

@@ -4,18 +4,21 @@ import path from 'node:path';
 import { stdin, stdout } from 'node:process';
 import { createInterface } from 'node:readline/promises';
 import { initializeDatabase } from './init.js';
-import { openConnection } from '../db/connection.js';
+import { databaseFileIdentity, openConnection } from '../db/connection.js';
 import { KiokukoError } from '../errors.js';
 import { BEGIN_MARKER, END_MARKER } from '../agent-file/managed-block.js';
 import { readProjectConfig } from '../config/project-config.js';
-import { getDatabaseLockPath, getRuntimeDescriptorPath } from '../config/paths.js';
+import { getDatabaseLockPath, getGlobalDatabasePath, getRuntimeDescriptorPath } from '../config/paths.js';
 import { listRepositoryLocations } from '../repository/binding.js';
 import { isPidAlive } from '../server/instance-lock.js';
 import { readRuntimeDescriptor } from '../server/runtime-descriptor.js';
 import { inspectLedger } from '../ledger/maintenance.js';
 import { findSecret } from '../memory/secrets.js';
 import { hybridSearchProjectionStatus } from '../memory/rebuild-search.js';
+import { requireHybridSearchProjectionSchema } from '../memory/structured-memory.js';
 import { readEntryRevision } from '../memory/revisions.js';
+import { inspectMigrationSnapshot, loadMigrationSnapshot } from '../db/migrate.js';
+import { inspectLegacyContextDeliveries } from '../context/delivery-migration.js';
 const MAX_DOCTOR_PROMPT_LOCATIONS = 20;
 /** Ask before removing registry rows for repository roots that no longer exist. */
 export async function promptRemoveMissingRepositoryLocations(locations, options = {}) {
@@ -46,6 +49,13 @@ export async function promptRemoveMissingRepositoryLocations(locations, options
 function count(database, sql, ...parameters) {
     return Number(database.prepare(sql).get(...parameters)?.count ?? 0);
 }
+function hasColumn(database, table, column) {
+    return Boolean(database.prepare('SELECT 1 AS present FROM pragma_table_info(?) WHERE name = ?').get(table, column));
+}
+function legacyDeliverySchemaIsInspectable(database) {
+    return hasColumn(database, 'context_deliveries', 'score_schema_version')
+        && hasColumn(database, 'context_delivery_entries', 'origin_scope');
+}
 function balancedMarkers(content) {
     return content.split(BEGIN_MARKER).length - 1 === 1 && content.split(END_MARKER).length - 1 === 1;
 }
@@ -96,64 +106,70 @@ async function runtimeCheck(databasePath, descriptorPath = getRuntimeDescriptorP
         findings += 1;
     return { ok: findings === 0, count: findings, detail: `findings=${findings}` };
 }
-export async function runDoctor(options = {}, dependencies = {}) {
-    const initialized = await initializeDatabase(options);
-    const database = (dependencies.openConnection ?? openConnection)(initialized.databasePath);
-    let doctorResult;
-    let operationFailed = false;
-    let operationError;
-    try {
-        const integrity = database.prepare('PRAGMA integrity_check').get()?.integrity_check ?? 'unknown';
-        const foreignKeyRows = database.prepare('PRAGMA foreign_key_check').all();
-        const fts5 = Boolean(database.prepare("SELECT 1 AS present FROM sqlite_master WHERE type = 'table' AND name = 'entries_fts'").get());
-        const migrationRows = count(database, 'SELECT COUNT(*) AS count FROM schema_migrations');
-        const expectedMigrations = initialized.currentVersion;
-        const migrationCheck = { ok: migrationRows === expectedMigrations, count: migrationRows, detail: `expected ${expectedMigrations}` };
-        const entryCount = count(database, 'SELECT COUNT(*) AS count FROM entries');
-        const ftsCount = fts5 ? count(database, 'SELECT COUNT(*) AS count FROM entries_fts') : 0;
-        let ftsCurrentMismatches = 0;
-        if (fts5) {
-            const currentRows = database.prepare(`
-        SELECT e.rowid, e.id, r.title, r.body, r.summary, e.current_revision
-          FROM entries e JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
-      `).all();
-            for (const row of currentRows) {
-                const projected = database.prepare('SELECT title, body, summary, tags_text FROM entries_fts WHERE rowid = ?').get(row.rowid);
-                const tags = database.prepare('SELECT tag FROM entry_revision_tags WHERE entry_id = ? AND revision = ? ORDER BY tag').all(row.id, row.current_revision).map((tag) => tag.tag);
-                if (!projected || projected.title !== row.title || projected.body !== row.body || projected.summary !== (row.summary ?? '') || projected.tags_text !== tags.join(' '))
-                    ftsCurrentMismatches += 1;
-            }
-        }
-        const ftsCheck = { ok: fts5 && entryCount === ftsCount && ftsCurrentMismatches === 0, count: Math.abs(entryCount - ftsCount) + ftsCurrentMismatches + (fts5 ? 0 : 1), detail: `present=${fts5}, entries=${entryCount}, fts=${ftsCount}, currentMismatches=${ftsCurrentMismatches}` };
-        const missingCurrentRevisions = count(database, `
-      SELECT COUNT(*) AS count FROM entries e
-      LEFT JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
-      WHERE r.entry_id IS NULL
-    `);
-        const orphanRevisionTags = count(database, `
-      SELECT COUNT(*) AS count FROM entry_revision_tags t
-      LEFT JOIN entry_revisions r ON r.entry_id = t.entry_id AND r.revision = t.revision
-      WHERE r.entry_id IS NULL
-    `);
-        const missingDeliveryRevisions = count(database, `
-      SELECT COUNT(*) AS count FROM context_delivery_entries d
-      LEFT JOIN entry_revisions r ON r.entry_id = d.entry_id AND r.revision = d.entry_revision
-      WHERE r.entry_id IS NULL
-    `);
-        const revisionRows = database.prepare(`
-      SELECT r.entry_id, r.workspace, r.revision
-        FROM entry_revisions AS r
+async function collectDoctorResult(database, options) {
+    const integrity = database.prepare('PRAGMA integrity_check').get()?.integrity_check ?? 'unknown';
+    const foreignKeyRows = database.prepare('PRAGMA foreign_key_check').all();
+    const currentMemoryFormatAvailable = options.databaseVersion >= 9;
+    const fts5 = Boolean(database.prepare("SELECT 1 AS present FROM sqlite_master WHERE type = 'table' AND name = 'entries_fts'").get());
+    const migrationRows = count(database, 'SELECT COUNT(*) AS count FROM schema_migrations');
+    const migrationCheck = { ok: migrationRows === options.currentVersion, count: migrationRows, detail: `expected ${options.currentVersion}` };
+    const entryCount = count(database, 'SELECT COUNT(*) AS count FROM entries');
+    const ftsCount = fts5 ? count(database, 'SELECT COUNT(*) AS count FROM entries_fts') : 0;
+    let ftsCurrentMismatches = 0;
+    if (fts5 && currentMemoryFormatAvailable) {
+        const currentRows = database.prepare(`
+      SELECT e.rowid, e.id, r.title, r.body, r.summary, e.current_revision
+        FROM entries e JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
     `).all();
-        const hashFormatTable = database.prepare(`
-      SELECT type
-        FROM sqlite_schema
-       WHERE name = 'entry_revision_hash_format'
-    `).get();
-        const hashFormats = hashFormatTable?.type === 'table'
-            ? database.prepare('SELECT singleton, algorithm FROM entry_revision_hash_format')
-                .all()
-            : [];
-        let revisionHashMismatches = hashFormats.length === 1
+        for (const row of currentRows) {
+            const projected = database.prepare('SELECT title, body, summary, tags_text FROM entries_fts WHERE rowid = ?').get(row.rowid);
+            const tags = database.prepare('SELECT tag FROM entry_revision_tags WHERE entry_id = ? AND revision = ? ORDER BY tag').all(row.id, row.current_revision).map((tag) => tag.tag);
+            if (!projected || projected.title !== row.title || projected.body !== row.body || projected.summary !== (row.summary ?? '') || projected.tags_text !== tags.join(' '))
+                ftsCurrentMismatches += 1;
+        }
+    }
+    const ftsCheck = !currentMemoryFormatAvailable
+        ? {
+            ok: fts5 && entryCount === ftsCount,
+            count: Math.abs(entryCount - ftsCount) + (fts5 ? 0 : 1),
+            detail: `present=${fts5}, entries=${entryCount}, fts=${ftsCount}, currentMismatches=deferred until migration 009`,
+        }
+        : {
+            ok: fts5 && entryCount === ftsCount && ftsCurrentMismatches === 0,
+            count: Math.abs(entryCount - ftsCount) + ftsCurrentMismatches + (fts5 ? 0 : 1),
+            detail: `present=${fts5}, entries=${entryCount}, fts=${ftsCount}, currentMismatches=${ftsCurrentMismatches}`,
+        };
+    const missingCurrentRevisions = count(database, `
+    SELECT COUNT(*) AS count FROM entries e
+    LEFT JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
+    WHERE r.entry_id IS NULL
+  `);
+    const orphanRevisionTags = count(database, `
+    SELECT COUNT(*) AS count FROM entry_revision_tags t
+    LEFT JOIN entry_revisions r ON r.entry_id = t.entry_id AND r.revision = t.revision
+    WHERE r.entry_id IS NULL
+  `);
+    const missingDeliveryRevisions = count(database, `
+    SELECT COUNT(*) AS count FROM context_delivery_entries d
+    LEFT JOIN entry_revisions r ON r.entry_id = d.entry_id AND r.revision = d.entry_revision
+    WHERE r.entry_id IS NULL
+  `);
+    const revisionRows = database.prepare(`
+    SELECT r.entry_id, r.workspace, r.revision
+      FROM entry_revisions AS r
+  `).all();
+    const hashFormatTable = database.prepare(`
+    SELECT type
+      FROM sqlite_schema
+     WHERE name = 'entry_revision_hash_format'
+  `).get();
+    const hashFormats = hashFormatTable?.type === 'table'
+        ? database.prepare('SELECT singleton, algorithm FROM entry_revision_hash_format')
+            .all()
+        : [];
+    let revisionHashMismatches = 0;
+    if (currentMemoryFormatAvailable) {
+        revisionHashMismatches = hashFormats.length === 1
             && hashFormats[0]?.singleton === 1
             && hashFormats[0].algorithm === 'canonical-json-utf16-tags-v1'
             ? 0
@@ -176,7 +192,24 @@ export async function runDoctor(options = {}, dependencies = {}) {
                 throw error;
             }
         }
-        const hybridCheck = (() => {
+    }
+    const revisionHashCheck = !currentMemoryFormatAvailable
+        ? { ok: true, count: 0, detail: 'current revision hashes deferred until migration 009' }
+        : { ok: revisionHashMismatches === 0, count: revisionHashMismatches };
+    const hybridCheck = !currentMemoryFormatAvailable
+        ? (() => {
+            try {
+                requireHybridSearchProjectionSchema(database);
+                return { ok: true, count: 0, detail: 'current projection contents deferred until migration 009' };
+            }
+            catch (error) {
+                if (error instanceof KiokukoError && error.code === 'INTEGRITY_ERROR') {
+                    return { ok: false, count: 1, detail: 'search projection schema is invalid' };
+                }
+                throw error;
+            }
+        })()
+        : (() => {
             try {
                 const projection = hybridSearchProjectionStatus(database);
                 return {
@@ -192,79 +225,175 @@ export async function runDoctor(options = {}, dependencies = {}) {
                 throw error;
             }
         })();
-        const danglingLinks = count(database, `
-      SELECT COUNT(*) AS count FROM entry_links l
-      LEFT JOIN entries f ON f.id = l.from_entry_id
-      LEFT JOIN entries t ON t.id = l.to_entry_id
-      WHERE f.id IS NULL OR t.id IS NULL
-    `);
-        const contradictions = count(database, `
-      SELECT COUNT(*) AS count FROM entry_links l
-      JOIN entries f ON f.id = l.from_entry_id
-      JOIN entries t ON t.id = l.to_entry_id
-      WHERE l.relation = 'contradicts' AND f.status = 'verified' AND t.status = 'verified'
-    `);
-        const bindingRows = listRepositoryLocations(database);
-        const missingRoots = bindingRows.filter((row) => !existsSync(row.canonicalRoot)).length;
-        const bindingCheck = { ok: missingRoots === 0, count: missingRoots, detail: `locations=${bindingRows.length}` };
-        let missingAgentFiles = 0;
-        for (const row of bindingRows) {
-            if (!existsSync(row.canonicalRoot))
-                continue;
-            const configPath = `${row.canonicalRoot}/.kiokuko.json`;
-            try {
-                const config = await readProjectConfig(configPath);
-                const agentPath = `${row.canonicalRoot}/${config.agentFile}`;
-                if (!existsSync(agentPath) || !balancedMarkers(readFileSync(agentPath, 'utf8')))
-                    missingAgentFiles += 1;
-            }
-            catch {
+    const danglingLinks = count(database, `
+    SELECT COUNT(*) AS count FROM entry_links l
+    LEFT JOIN entries f ON f.id = l.from_entry_id
+    LEFT JOIN entries t ON t.id = l.to_entry_id
+    WHERE f.id IS NULL OR t.id IS NULL
+  `);
+    const contradictions = count(database, `
+    SELECT COUNT(*) AS count FROM entry_links l
+    JOIN entries f ON f.id = l.from_entry_id
+    JOIN entries t ON t.id = l.to_entry_id
+    WHERE l.relation = 'contradicts' AND f.status = 'verified' AND t.status = 'verified'
+  `);
+    const bindingRows = listRepositoryLocations(database);
+    const missingRoots = bindingRows.filter((row) => !existsSync(row.canonicalRoot)).length;
+    const bindingCheck = { ok: missingRoots === 0, count: missingRoots, detail: `locations=${bindingRows.length}` };
+    let missingAgentFiles = 0;
+    for (const row of bindingRows) {
+        if (!existsSync(row.canonicalRoot))
+            continue;
+        const configPath = `${row.canonicalRoot}/.kiokuko.json`;
+        try {
+            const config = await readProjectConfig(configPath);
+            const agentPath = `${row.canonicalRoot}/${config.agentFile}`;
+            if (!existsSync(agentPath) || !balancedMarkers(readFileSync(agentPath, 'utf8')))
                 missingAgentFiles += 1;
-            }
         }
-        const agentFilesCheck = { ok: missingAgentFiles === 0, count: missingAgentFiles };
-        let secretCount = 0;
-        const secretRows = database.prepare(`
-      SELECT r.title, r.body, r.summary, r.scope_json, r.provenance_json
-        FROM entries e JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
-    `).all();
-        for (const row of secretRows) {
-            if (findSecret(`${row.title}\n${row.body}\n${row.summary ?? ''}\n${row.scope_json}\n${row.provenance_json}`))
-                secretCount += 1;
+        catch {
+            missingAgentFiles += 1;
         }
-        const permissions = (() => {
-            try {
-                const mode = statSync(initialized.databasePath).mode & 0o777;
-                return { ok: (mode & 0o077) === 0, count: mode, detail: `mode=${mode.toString(8)}` };
-            }
-            catch {
-                return { ok: false, count: 0, detail: 'database file is not accessible' };
+    }
+    const agentFilesCheck = { ok: missingAgentFiles === 0, count: missingAgentFiles };
+    let secretCount = 0;
+    const secretRows = database.prepare(`
+    SELECT r.title, r.body, r.summary, r.scope_json, r.provenance_json
+      FROM entries e JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
+  `).all();
+    for (const row of secretRows) {
+        if (findSecret(`${row.title}\n${row.body}\n${row.summary ?? ''}\n${row.scope_json}\n${row.provenance_json}`))
+            secretCount += 1;
+    }
+    const permissions = (() => {
+        try {
+            const mode = statSync(options.databasePath).mode & 0o777;
+            return { ok: (mode & 0o077) === 0, count: mode, detail: `mode=${mode.toString(8)}` };
+        }
+        catch {
+            return { ok: false, count: 0, detail: 'database file is not accessible' };
+        }
+    })();
+    const ledgerReport = inspectLedger(database);
+    const ledgerCheck = { ok: ledgerReport.ok, count: ledgerReport.findingCount, detail: `findings=${ledgerReport.findingCount}` };
+    const nudgeDeliveries = {
+        ok: ledgerReport.checks.nudgeDeliveries.ok,
+        count: ledgerReport.checks.nudgeDeliveries.findingCount,
+        detail: `deliveries=${ledgerReport.counts.nudgeDeliveries}, findings=${ledgerReport.checks.nudgeDeliveries.findingCount}`,
+    };
+    const legacyDeliveriesTruncated = options.legacyDeliveries.scanTruncated
+        || options.legacyDeliveries.findingsTruncated;
+    const legacyDeliveries = {
+        ok: options.legacyDeliveries.invalid === 0 && !legacyDeliveriesTruncated,
+        count: options.legacyDeliveries.invalid + (legacyDeliveriesTruncated ? 1 : 0),
+        detail: `scanned=${options.legacyDeliveries.scanned}, valid=${options.legacyDeliveries.valid}, invalid=${options.legacyDeliveries.invalid}, findings=${options.legacyDeliveries.findings.length}, scanTruncated=${options.legacyDeliveries.scanTruncated}, findingsTruncated=${options.legacyDeliveries.findingsTruncated}`,
+    };
+    const runtime = await runtimeCheck(options.databasePath, options.runtimeDescriptorPath);
+    const checks = {
+        integrity: { ok: integrity === 'ok', detail: integrity },
+        foreignKeys: { ok: foreignKeyRows.length === 0, count: foreignKeyRows.length },
+        entryRevisions: { ok: missingCurrentRevisions === 0, count: missingCurrentRevisions },
+        revisionTags: { ok: orphanRevisionTags === 0, count: orphanRevisionTags },
+        deliveryRevisions: { ok: missingDeliveryRevisions === 0, count: missingDeliveryRevisions },
+        revisionHashes: revisionHashCheck,
+        migrations: migrationCheck,
+        fts: ftsCheck,
+        danglingLinks: { ok: danglingLinks === 0, count: danglingLinks },
+        contradictions: { ok: contradictions === 0, count: contradictions, detail: 'verified contradictions require review' },
+        bindings: bindingCheck,
+        agentFiles: agentFilesCheck,
+        permissions,
+        secrets: { ok: secretCount === 0, count: secretCount },
+        ledger: ledgerCheck,
+        nudgeDeliveries,
+        legacyDeliveries,
+        runtime,
+        hybridSearch: hybridCheck,
+    };
+    const ok = Object.values(checks).every((check) => check.ok);
+    return {
+        ok,
+        databasePath: '<redacted>',
+        currentVersion: options.currentVersion,
+        capabilities: options.capabilities,
+        legacyDeliveries: options.legacyDeliveries,
+        integrity,
+        fts5,
+        checks,
+    };
+}
+async function legacyMigrationPreflight(options) {
+    const databasePath = options.databasePath ?? getGlobalDatabasePath();
+    if (databasePath === ':memory:')
+        return undefined;
+    let identity;
+    try {
+        identity = databaseFileIdentity(databasePath);
+    }
+    catch {
+        return undefined;
+    }
+    const database = openConnection(databasePath, { readOnly: true, expectedFileIdentity: identity });
+    let operationFailed = false;
+    let operationError;
+    let result;
+    try {
+        const snapshot = loadMigrationSnapshot(options.migrationsDirectory);
+        const plan = inspectMigrationSnapshot(database, snapshot);
+        if (plan.pending.includes(12) && legacyDeliverySchemaIsInspectable(database)) {
+            const report = inspectLegacyContextDeliveries(database);
+            if (report.invalid > 0 || report.scanTruncated || report.findingsTruncated) {
+                result = await collectDoctorResult(database, {
+                    databasePath,
+                    databaseVersion: plan.databaseVersion,
+                    currentVersion: plan.currentVersion,
+                    capabilities: null,
+                    ...(options.runtimeDescriptorPath === undefined ? {} : { runtimeDescriptorPath: options.runtimeDescriptorPath }),
+                    legacyDeliveries: report,
+                });
             }
-        })();
-        const ledgerReport = inspectLedger(database);
-        const ledgerCheck = { ok: ledgerReport.ok, count: ledgerReport.findingCount, detail: `findings=${ledgerReport.findingCount}` };
-        const runtime = await runtimeCheck(initialized.databasePath, options.runtimeDescriptorPath);
-        const checks = {
-            integrity: { ok: integrity === 'ok', detail: integrity },
-            foreignKeys: { ok: foreignKeyRows.length === 0, count: foreignKeyRows.length },
-            entryRevisions: { ok: missingCurrentRevisions === 0, count: missingCurrentRevisions },
-            revisionTags: { ok: orphanRevisionTags === 0, count: orphanRevisionTags },
-            deliveryRevisions: { ok: missingDeliveryRevisions === 0, count: missingDeliveryRevisions },
-            revisionHashes: { ok: revisionHashMismatches === 0, count: revisionHashMismatches },
-            migrations: migrationCheck,
-            fts: ftsCheck,
-            danglingLinks: { ok: danglingLinks === 0, count: danglingLinks },
-            contradictions: { ok: contradictions === 0, count: contradictions, detail: 'verified contradictions require review' },
-            bindings: bindingCheck,
-            agentFiles: agentFilesCheck,
-            permissions,
-            secrets: { ok: secretCount === 0, count: secretCount },
-            ledger: ledgerCheck,
-            runtime,
-            hybridSearch: hybridCheck,
-        };
-        const ok = Object.values(checks).every((check) => check.ok);
-        doctorResult = { ok, databasePath: '<redacted>', currentVersion: initialized.currentVersion, capabilities: initialized.capabilities, integrity, fts5, checks };
+        }
+    }
+    catch (error) {
+        operationFailed = true;
+        operationError = error;
+    }
+    try {
+        database.close();
+    }
+    catch (closeError) {
+        if (operationFailed) {
+            throw new AggregateError([operationError, closeError], 'Doctor legacy preflight failed and closing the database connection also failed');
+        }
+        throw closeError;
+    }
+    if (operationFailed)
+        throw operationError;
+    return result;
+}
+export async function runDoctor(options = {}, dependencies = {}) {
+    const preflight = await legacyMigrationPreflight(options);
+    if (preflight !== undefined)
+        return preflight;
+    const initOptions = {
+        ...(options.databasePath === undefined ? {} : { databasePath: options.databasePath }),
+        ...(options.migrationsDirectory === undefined ? {} : { migrationsDirectory: options.migrationsDirectory }),
+    };
+    const initialized = await initializeDatabase(initOptions);
+    const database = (dependencies.openConnection ?? openConnection)(initialized.databasePath);
+    let doctorResult;
+    let operationFailed = false;
+    let operationError;
+    try {
+        const legacyDeliveries = inspectLegacyContextDeliveries(database);
+        doctorResult = await collectDoctorResult(database, {
+            databasePath: initialized.databasePath,
+            databaseVersion: initialized.currentVersion,
+            currentVersion: initialized.currentVersion,
+            capabilities: initialized.capabilities,
+            ...(options.runtimeDescriptorPath === undefined ? {} : { runtimeDescriptorPath: options.runtimeDescriptorPath }),
+            legacyDeliveries,
+        });
     }
     catch (error) {
         operationFailed = true;

package/dist/commands/doctor.js.map

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

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

@@ -17,6 +17,7 @@ import { detectInstalledClients } from '../setup/client-detection.js';
 import { assertExactLegacyOpenCodeLoopGuard, cleanupLegacyClaudePromptHook, } from '../setup/legacy-client-cleanup.js';
 import { loadBundledStandardSkillFiles, renderStandardSkillFile, } from '../setup/standard-skills.js';
 import { listRegisteredProjectLocations, refreshRegisteredProjectAgentFiles, } from '../setup/project-agent-refresh.js';
+import { findMissingRepositoryLocations, removeMissingRepositoryLocations, } from '../repository/binding.js';
 export const SETUP_CLIENTS = ['codex', 'opencode', 'claude', 'hermes'];
 function setupPathJoin(options, ...segments) {
     const platform = options.platform ?? process.platform;
@@ -568,6 +569,8 @@ export async function setupGlobalClients(options = {}, dependencyOverrides = {})
     let workspaceInitializationFailed = false;
     let workspaceInitializationError;
     try {
+        const missingProjectLocations = findMissingRepositoryLocations(database);
+        removeMissingRepositoryLocations(database, missingProjectLocations);
         dependencies.ensureGlobalWorkspace(database);
         registeredProjectLocations = listRegisteredProjectLocations(database, {
             allowUnavailableRegistry: options.migrationsDirectory !== undefined,