kiokuko 1.0.0

package/dist/commands/doctor.js

@@ -0,0 +1,389 @@
+import { createHash } from 'node:crypto';
+import { existsSync, lstatSync, readFileSync, statSync } from 'node:fs';
+import path from 'node:path';
+import { stdin, stdout } from 'node:process';
+import { createInterface } from 'node:readline/promises';
+import { readRegularFile } from '../agent-file/atomic-write.js';
+import { BEGIN_MARKER, END_MARKER } from '../agent-file/managed-block.js';
+import { getCodexConfigPath, getDatabaseLockPath, getRuntimeDescriptorPath } from '../config/paths.js';
+import { readProjectConfig } from '../config/project-config.js';
+import { openConnection } from '../db/connection.js';
+import { EmbeddingBackendUnavailableError, openEmbeddingDatabase } from '../embedding/backend.js';
+import { parseEmbeddingConfig } from '../embedding/config.js';
+import { inspectEmbeddingHealth } from '../embedding/diagnostics.js';
+import { readPersistedEmbeddingSettings } from '../embedding/settings.js';
+import { KiokukoError } from '../errors.js';
+import { inspectLedger } from '../ledger/maintenance.js';
+import { hybridSearchProjectionStatus } from '../memory/rebuild-search.js';
+import { readEntryRevision } from '../memory/revisions.js';
+import { findSecret } from '../memory/secrets.js';
+import { listRepositoryLocations } from '../repository/binding.js';
+import { isPidAlive } from '../server/instance-lock.js';
+import { readRuntimeDescriptor } from '../server/runtime-descriptor.js';
+import { setupMcpIdentityConflictClient } from '../setup/mcp-conflict.js';
+import { renderCodexMcpConfig } from '../setup/render.js';
+import { initializeDatabase } from './init.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 = {}) {
+    if (locations.length < 1) {
+        throw new KiokukoError('VALIDATION_ERROR', 'Missing repository locations must not be empty');
+    }
+    const input = options.input ?? stdin;
+    const output = options.output ?? stdout;
+    const prompt = createInterface({ input, output });
+    try {
+        const count = locations.length;
+        output.write(`Doctor found ${count} repository location${count === 1 ? '' : 's'} with a missing root. `
+            + 'The following registry rows are candidates:\n');
+        for (const location of locations.slice(0, MAX_DOCTOR_PROMPT_LOCATIONS)) {
+            output.write(`  - ${location.canonicalRoot}\n`);
+        }
+        if (locations.length > MAX_DOCTOR_PROMPT_LOCATIONS) {
+            output.write(`  ... and ${locations.length - MAX_DOCTOR_PROMPT_LOCATIONS} more\n`);
+        }
+        output.write('This removes registry rows only; it does not delete files or memory.\n');
+        const answer = (await prompt.question('Remove these stale locations? [Y/n] ')).trim();
+        return answer.length === 0 || /^(?:y|yes|はい)$/iu.test(answer);
+    }
+    finally {
+        prompt.close();
+    }
+}
+function count(database, sql, ...parameters) {
+    return Number(database.prepare(sql).get(...parameters)?.count ?? 0);
+}
+function balancedMarkers(content) {
+    return content.split(BEGIN_MARKER).length - 1 === 1 && content.split(END_MARKER).length - 1 === 1;
+}
+/** Inspect the Codex MCP identity using the same canonical parser as setup. */
+async function codexMcpCheck() {
+    let config;
+    try {
+        config = await readRegularFile(getCodexConfigPath());
+    }
+    catch {
+        return { ok: false, count: 1, detail: 'config=unavailable' };
+    }
+    if (config === undefined)
+        return { ok: true, count: 0, detail: 'config=absent' };
+    try {
+        // Rendering is intentionally discarded: it validates the existing identity
+        // without writing, and accepts configs that simply have not been configured.
+        renderCodexMcpConfig(config.content);
+        return { ok: true, count: 0, detail: 'config=canonical-or-not-configured' };
+    }
+    catch (error) {
+        if (setupMcpIdentityConflictClient(error) === 'codex') {
+            return { ok: false, count: 1, detail: 'config=conflict' };
+        }
+        return { ok: false, count: 1, detail: 'config=invalid' };
+    }
+}
+function skippedCodexMcpCheck() {
+    return { ok: true, count: 0, detail: 'config=skipped-for-explicit-database' };
+}
+async function runtimeCheck(databasePath, descriptorPath = getRuntimeDescriptorPath()) {
+    let findings = 0;
+    let descriptor;
+    let descriptorPresent = false;
+    let lockPresent = false;
+    try {
+        descriptor = await readRuntimeDescriptor(descriptorPath);
+        if (descriptor !== undefined) {
+            const expected = `sha256:${createHash('sha256').update(path.resolve(databasePath), 'utf8').digest('hex')}`;
+            // A single runtime descriptor is shared by the normal CLI/server
+            // installation. It may legitimately describe another database when
+            // doctor is run against an explicit backup or test database.
+            if (descriptor.databaseFingerprint === expected) {
+                descriptorPresent = true;
+                if (!(await isPidAlive(descriptor.pid)))
+                    findings += 1;
+            }
+        }
+    }
+    catch {
+        findings += 1;
+    }
+    const lockPath = getDatabaseLockPath(databasePath);
+    try {
+        const info = lstatSync(lockPath);
+        lockPresent = true;
+        if (info.isSymbolicLink() || !info.isFile() || (process.platform !== 'win32' && (info.mode & 0o077) !== 0))
+            findings += 1;
+        try {
+            const value = JSON.parse(readFileSync(lockPath, 'utf8'));
+            if (typeof value.instanceId !== 'string' || typeof value.pid !== 'number' || !(await isPidAlive(value.pid)))
+                findings += 1;
+            if (descriptor !== undefined && value.instanceId !== descriptor.instanceId)
+                findings += 1;
+        }
+        catch {
+            findings += 1;
+        }
+    }
+    catch (error) {
+        if (!(error instanceof Error && 'code' in error && error.code === 'ENOENT'))
+            findings += 1;
+    }
+    if (descriptorPresent !== lockPresent)
+        findings += 1;
+    return { ok: findings === 0, count: findings, detail: `findings=${findings}` };
+}
+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 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 ${options.currentVersion}` };
+    const entryCount = count(database, 'SELECT COUNT(*) AS count FROM entries');
+    const ftsCount = fts5 ? count(database, 'SELECT COUNT(*) AS count FROM entries_fts') : 0;
+    let ftsCurrentMismatches = 0;
+    if (fts5) {
+        const currentRows = database.prepare(`
+      SELECT e.rowid, e.id, r.title, r.body, r.summary, e.current_revision
+        FROM entries e JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
+    `).all();
+        for (const row of currentRows) {
+            const projected = database.prepare('SELECT title, body, summary, tags_text FROM entries_fts WHERE rowid = ?').get(row.rowid);
+            const tags = database.prepare('SELECT tag FROM entry_revision_tags WHERE entry_id = ? AND revision = ? ORDER BY tag').all(row.id, row.current_revision).map((tag) => tag.tag);
+            if (!projected || projected.title !== row.title || projected.body !== row.body || projected.summary !== (row.summary ?? '') || projected.tags_text !== tags.join(' '))
+                ftsCurrentMismatches += 1;
+        }
+    }
+    const ftsCheck = {
+        ok: fts5 && entryCount === ftsCount && ftsCurrentMismatches === 0,
+        count: Math.abs(entryCount - ftsCount) + ftsCurrentMismatches + (fts5 ? 0 : 1),
+        detail: `present=${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
+  `).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;
+    revisionHashMismatches = hashFormats.length === 1
+        && hashFormats[0]?.singleton === 1
+        && hashFormats[0].algorithm === 'canonical-json-utf16-tags-v1'
+        ? 0
+        : 1;
+    for (const row of revisionRows) {
+        try {
+            // The shared decoder accepts only the canonical JSON preimage and the
+            // single locale-independent revision hash format.
+            readEntryRevision(database, {
+                entryId: row.entry_id,
+                workspace: row.workspace,
+                revision: row.revision,
+            });
+        }
+        catch (error) {
+            if (error instanceof KiokukoError && error.code === 'INTEGRITY_ERROR') {
+                revisionHashMismatches += 1;
+                continue;
+            }
+            throw error;
+        }
+    }
+    const revisionHashCheck = { ok: revisionHashMismatches === 0, count: revisionHashMismatches };
+    const hybridCheck = (() => {
+        try {
+            const projection = hybridSearchProjectionStatus(database);
+            return {
+                ok: projection.missingSignals === 0 && projection.extraSignals === 0 && projection.staleTrigram === 0,
+                count: projection.missingSignals + projection.extraSignals + projection.staleTrigram,
+                detail: `entries=${projection.entries}, trigram=${projection.trigram}, signals=${projection.signals}, missingSignals=${projection.missingSignals}, extraSignals=${projection.extraSignals}, staleTrigram=${projection.staleTrigram}`,
+            };
+        }
+        catch (error) {
+            if (error instanceof KiokukoError && error.code === 'INTEGRITY_ERROR') {
+                return { ok: false, count: 1, detail: 'stored projection source is invalid' };
+            }
+            throw error;
+        }
+    })();
+    const danglingLinks = count(database, `
+    SELECT COUNT(*) AS count FROM entry_links l
+    LEFT JOIN entries f ON f.id = l.from_entry_id
+    LEFT JOIN entries t ON t.id = l.to_entry_id
+    WHERE f.id IS NULL OR t.id IS NULL
+  `);
+    const contradictions = count(database, `
+    SELECT COUNT(*) AS count FROM entry_links l
+    JOIN entries f ON f.id = l.from_entry_id
+    JOIN entries t ON t.id = l.to_entry_id
+    WHERE l.relation = 'contradicts' AND f.status = 'verified' AND t.status = 'verified'
+  `);
+    const bindingRows = listRepositoryLocations(database);
+    const missingRoots = bindingRows.filter((row) => !existsSync(row.canonicalRoot)).length;
+    const bindingCheck = { ok: missingRoots === 0, count: missingRoots, detail: `locations=${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}/${config.agentFile}`;
+            if (!existsSync(agentPath) || !balancedMarkers(readFileSync(agentPath, 'utf8')))
+                missingAgentFiles += 1;
+        }
+        catch {
+            missingAgentFiles += 1;
+        }
+    }
+    const agentFilesCheck = { ok: missingAgentFiles === 0, count: missingAgentFiles };
+    let secretCount = 0;
+    const secretRows = database.prepare(`
+    SELECT r.title, r.body, r.summary, r.scope_json, r.provenance_json
+      FROM entries e JOIN entry_revisions r ON r.entry_id = e.id AND r.revision = e.current_revision
+  `).all();
+    for (const row of secretRows) {
+        if (findSecret(`${row.title}\n${row.body}\n${row.summary ?? ''}\n${row.scope_json}\n${row.provenance_json}`))
+            secretCount += 1;
+    }
+    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 runtime = await runtimeCheck(options.databasePath, options.runtimeDescriptorPath);
+    const embeddings = inspectEmbeddingHealth(database, options.embeddingEnvironment ?? readPersistedEmbeddingSettings(database), options.embeddingBackend);
+    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,
+        runtime,
+        hybridSearch: hybridCheck,
+        embeddings: embeddings.check,
+        codexMcp: options.codexMcp,
+    };
+    const ok = Object.values(checks).every((check) => check.ok);
+    return {
+        ok,
+        databasePath: '<redacted>',
+        currentVersion: options.currentVersion,
+        capabilities: options.capabilities,
+        integrity,
+        fts5,
+        checks,
+    };
+}
+export async function runDoctor(options = {}, dependencies = {}) {
+    const initOptions = {
+        ...(options.databasePath === undefined ? {} : { databasePath: options.databasePath }),
+        ...(options.migrationsDirectory === undefined ? {} : { migrationsDirectory: options.migrationsDirectory }),
+    };
+    const initialized = await initializeDatabase(initOptions);
+    const codexMcp = options.databasePath === undefined ? await codexMcpCheck() : skippedCodexMcpCheck();
+    let embeddingConfig;
+    try {
+        embeddingConfig = options.embeddingEnvironment === undefined
+            ? undefined
+            : parseEmbeddingConfig(options.embeddingEnvironment);
+    }
+    catch {
+        embeddingConfig = undefined;
+    }
+    let opened;
+    try {
+        opened = await openEmbeddingDatabase(initialized.databasePath, {
+            ...(embeddingConfig === undefined ? {} : { config: embeddingConfig }),
+            openDatabase: dependencies.openConnection ?? openConnection,
+            ...(options.embeddingBackend === undefined ? {} : { backend: options.embeddingBackend }),
+        });
+    }
+    catch (error) {
+        if (!(error instanceof EmbeddingBackendUnavailableError))
+            throw error;
+        opened = {
+            database: (dependencies.openConnection ?? openConnection)(initialized.databasePath),
+            backend: undefined,
+        };
+    }
+    const database = opened.database;
+    let doctorResult;
+    let operationFailed = false;
+    let operationError;
+    try {
+        doctorResult = await collectDoctorResult(database, {
+            databasePath: initialized.databasePath,
+            databaseVersion: initialized.currentVersion,
+            currentVersion: initialized.currentVersion,
+            capabilities: initialized.capabilities,
+            ...(options.runtimeDescriptorPath === undefined ? {} : { runtimeDescriptorPath: options.runtimeDescriptorPath }),
+            ...(options.embeddingEnvironment === undefined ? {} : { embeddingEnvironment: options.embeddingEnvironment }),
+            ...((opened.backend ?? options.embeddingBackend) === undefined
+                ? {}
+                : { embeddingBackend: opened.backend ?? options.embeddingBackend }),
+            codexMcp,
+        });
+    }
+    catch (error) {
+        operationFailed = true;
+        operationError = error;
+    }
+    try {
+        database.close();
+    }
+    catch (closeError) {
+        if (operationFailed) {
+            throw new AggregateError([operationError, closeError], 'Doctor checks failed and closing the database connection also failed');
+        }
+        throw closeError;
+    }
+    if (operationFailed)
+        throw operationError;
+    if (doctorResult === undefined) {
+        throw new KiokukoError('INTEGRITY_ERROR', 'Doctor checks produced no result');
+    }
+    return doctorResult;
+}
+//# sourceMappingURL=doctor.js.map

package/dist/commands/doctor.js.map

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package/dist/commands/embeddings.d.ts

@@ -0,0 +1,40 @@
+import type { Command } from 'commander';
+import type { PathEnvironment } from '../config/paths.js';
+import type { SqliteDatabase } from '../db/adapter.js';
+import type { ModelDownloader } from '../embedding/model-download.js';
+import type { InstalledModel } from '../embedding/model-installation.js';
+import { runEmbeddingSetup } from '../embedding/setup-service.js';
+import type { EmbeddingProvider, VectorSearchBackend } from '../embedding/types.js';
+import { type SetupOptions, type SetupResult } from './setup.js';
+export interface OptionalRuntimeInstallInvocation {
+    readonly command: 'npm' | 'sudo';
+    readonly args: readonly string[];
+    readonly cwd?: string;
+}
+/** Select the npm invocation without assuming that every Unix prefix needs root. */
+export declare function optionalRuntimeInstallInvocation(platform?: NodeJS.Platform, packageRoot?: string): OptionalRuntimeInstallInvocation;
+export type EmbeddingsDatabaseRunner = <T>(operation: (database: SqliteDatabase, backend?: VectorSearchBackend) => T | Promise<T>) => Promise<T>;
+export type EmbeddingsOutput = (json: boolean | undefined, operation: string, data: unknown, message: string, meta?: Record<string, unknown>) => void;
+export type EmbeddingsOptionalRuntimeChecker = () => Promise<void>;
+export interface EmbeddingsSignalSource {
+    once(signal: 'SIGINT' | 'SIGTERM', listener: () => void): unknown;
+    off(signal: 'SIGINT' | 'SIGTERM', listener: () => void): unknown;
+}
+export interface EmbeddingsCommandDependencies {
+    readonly withDatabase: EmbeddingsDatabaseRunner;
+    readonly environment?: NodeJS.ProcessEnv;
+    readonly optionalRuntimeChecker?: EmbeddingsOptionalRuntimeChecker;
+    readonly optionalRuntimeInstaller?: () => Promise<void>;
+    readonly provider?: EmbeddingProvider;
+    readonly backend?: VectorSearchBackend;
+    readonly output?: EmbeddingsOutput;
+    readonly signals?: EmbeddingsSignalSource;
+    readonly modelDownloader?: ModelDownloader;
+    readonly modelInstaller?: (preset: typeof import('../embedding/presets/local-small.js').LOCAL_SMALL_PRESET, options: Parameters<typeof runEmbeddingSetup>[2]) => Promise<InstalledModel>;
+    readonly pathEnvironment?: PathEnvironment;
+    readonly setupInput?: NodeJS.ReadableStream;
+    readonly setupOutput?: NodeJS.WritableStream;
+    readonly setupGlobalClients?: (options: SetupOptions) => Promise<Pick<SetupResult, 'clients' | 'projectAgentFiles'>>;
+}
+export declare function registerEmbeddingsCommands(cli: Command, dependencies: EmbeddingsCommandDependencies): Command;
+//# sourceMappingURL=embeddings.d.ts.map

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

@@ -0,0 +1 @@
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