@askdkc/kiokuko 0.1.19 → 0.1.21

package/dist/memory/entries.js

@@ -1,6 +1,6 @@
 import { randomUUID } from 'node:crypto';
 import { withImmediateTransaction } from '../db/transaction.js';
-import { KiokukoError } from '../errors.js';
+import { KiokukoError, storedMemoryIntegrityError } from '../errors.js';
 import { canonicalEntryRevisionContentHash, canonicalJson, validateRecordInput, requireWorkspace } from '../serialization/validate.js';
 import { recordAuditEvent } from './audit.js';
 import { findSecret } from './secrets.js';
@@ -8,7 +8,7 @@ import { syncEntrySearchProjection } from './structured-memory.js';
 import { decodeStoredMemoryRow, insertEntryRevisionInTransaction, normalizeStructuredScopeInput } from './revisions.js';
 function rowToEntry(database, row, options = {}) {
     if (typeof row.revision_entry_id !== 'string' || !Number.isSafeInteger(row.current_revision)) {
-        throw new KiokukoError('INTEGRITY_ERROR', 'Stored entry or revision is invalid');
+        throw storedMemoryIntegrityError();
     }
     const tags = database
         .prepare('SELECT tag FROM entry_revision_tags WHERE entry_id = ? AND revision = ? ORDER BY tag ASC')
@@ -51,7 +51,7 @@ function rowToEntry(database, row, options = {}) {
     });
     const entry = decoded.entry;
     if (entry === undefined)
-        throw new KiokukoError('INTEGRITY_ERROR', 'Stored entry or revision is invalid');
+        throw storedMemoryIntegrityError();
     const revision = decoded.revision;
     return {
         id: entry.id,

package/dist/memory/entries.js.map

@@ -1 +1 @@
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package/dist/memory/revisions.d.ts

@@ -95,15 +95,19 @@ export declare function decodeStoredMemoryRow(input: {
     revision: EntryRevisionRecord;
     entry?: DecodedStoredEntryValues;
 };
+export interface RevisionHashMigrationOptions {
+    readonly recoverInvalidStoredMemory?: boolean;
+}
 /**
  * One-time migration operation for migration 009. This is the only place that
  * recognizes the released locale-dependent hash preimage. The caller must own
  * the migration transaction; any invalid preimage or canonical collision
  * aborts the whole schema upgrade.
  */
-export declare function canonicalizeEntryRevisionHashesInMigration(database: SqliteDatabase): {
+export declare function canonicalizeEntryRevisionHashesInMigration(database: SqliteDatabase, options?: RevisionHashMigrationOptions): {
     inspected: number;
     rewritten: number;
+    recoveredEntries: number;
 };
 export declare function readEntryRevision(database: SqliteDatabase, input: {
     entryId: string;

package/dist/memory/revisions.d.ts.map

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package/dist/memory/revisions.js

@@ -1,4 +1,4 @@
-import { KiokukoError } from '../errors.js';
+import { KiokukoError, storedMemoryIntegrityError } from '../errors.js';
 import { canonicalContentHash, canonicalEntryRevisionContentHash, canonicalJson, ENTRY_STATUSES, requireWorkspace, TRUST_LEVELS, validateRecordInput, } from '../serialization/validate.js';
 import { buildStructuredScope, } from './structured-memory.js';
 const SQLITE_CONSTRAINT_PRIMARY_KEY = 1_555;
@@ -16,7 +16,7 @@ function isExpectedRevisionConflict(error) {
         && REVISION_UNIQUENESS_FAILURES.has(failure.message);
 }
 function storedIntegrity() {
-    throw new KiokukoError('INTEGRITY_ERROR', 'Stored entry or revision is invalid');
+    throw storedMemoryIntegrityError();
 }
 function isPlainObject(value) {
     if (typeof value !== 'object' || value === null || Array.isArray(value))
@@ -308,6 +308,118 @@ BEFORE UPDATE ON entry_revisions
 BEGIN
     SELECT RAISE(ABORT, 'entry_revisions are immutable');
 END`;
+function quoteSqlIdentifier(value) {
+    return `"${value.replaceAll('"', '""')}"`;
+}
+function tableNames(database) {
+    return database
+        .prepare(`
+      SELECT name
+        FROM sqlite_schema
+       WHERE type = 'table'
+         AND name NOT LIKE 'sqlite_%'
+    `)
+        .all()
+        .flatMap((row) => typeof row.name === 'string' ? [row.name] : []);
+}
+function foreignKeys(database, table) {
+    return database
+        .prepare(`PRAGMA foreign_key_list(${quoteSqlIdentifier(table)})`)
+        .all();
+}
+function recoveryEntryId(row) {
+    if (typeof row.id !== 'string' || row.id.length === 0 || typeof row.workspace !== 'string') {
+        storedIntegrity();
+    }
+    return row.id;
+}
+function invalidRecoveryRevisionRows(database, entryId) {
+    return database
+        .prepare(`
+      SELECT entry_id AS entryId, revision
+        FROM entry_revisions
+       WHERE entry_id = ?
+       ORDER BY revision
+    `)
+        .all(entryId);
+}
+function deleteForeignKeyReferences(database, invalidEntries) {
+    const entryIds = invalidEntries.map(recoveryEntryId);
+    const revisions = invalidEntries.flatMap((entry) => invalidRecoveryRevisionRows(database, recoveryEntryId(entry)));
+    for (const table of tableNames(database)) {
+        for (const foreignKey of foreignKeys(database, table)) {
+            if (typeof foreignKey.table !== 'string' || typeof foreignKey.from !== 'string'
+                || typeof foreignKey.to !== 'string')
+                continue;
+            const childTable = quoteSqlIdentifier(table);
+            const childColumn = quoteSqlIdentifier(foreignKey.from);
+            if (foreignKey.table === 'entries' && foreignKey.to === 'id') {
+                for (const entryId of entryIds) {
+                    if (table === 'entries' && foreignKey.from === 'superseded_by') {
+                        database.prepare(`
+              UPDATE entries
+                 SET superseded_by = NULL,
+                     status = CASE WHEN status = 'superseded' THEN 'candidate' ELSE status END,
+                     verified_at = CASE WHEN status = 'superseded' THEN NULL ELSE verified_at END
+               WHERE ${childColumn} = ?
+            `).run(entryId);
+                    }
+                    else if (table !== 'entries' && table !== 'entry_revisions') {
+                        database.prepare(`DELETE FROM ${childTable} WHERE ${childColumn} = ?`).run(entryId);
+                    }
+                }
+            }
+            else if (foreignKey.table === 'entry_revisions'
+                && (foreignKey.to === 'entry_id' || foreignKey.to === 'revision')) {
+                // Composite foreign keys are removed as one group below. Processing
+                // only their first column here would leave unrelated revision rows
+                // vulnerable to an over-broad delete.
+                continue;
+            }
+        }
+        const groups = new Map();
+        for (const foreignKey of foreignKeys(database, table)) {
+            if (typeof foreignKey.id !== 'number' || typeof foreignKey.table !== 'string')
+                continue;
+            const key = `${foreignKey.id}\u0000${foreignKey.table}`;
+            const group = groups.get(key) ?? [];
+            group.push(foreignKey);
+            groups.set(key, group);
+        }
+        for (const group of groups.values()) {
+            if (group[0]?.table !== 'entry_revisions' || table === 'entry_revisions')
+                continue;
+            const columns = group
+                .map((foreignKey) => ({
+                from: foreignKey.from,
+                to: foreignKey.to,
+            }))
+                .filter((value) => typeof value.from === 'string' && (value.to === 'entry_id' || value.to === 'revision'));
+            if (columns.length !== group.length)
+                continue;
+            for (const revision of revisions) {
+                if (typeof revision.entryId !== 'string' || typeof revision.revision !== 'number')
+                    continue;
+                const parameters = columns.map(({ to }) => to === 'entry_id' ? revision.entryId : revision.revision);
+                const predicate = columns.map(({ from }) => `${quoteSqlIdentifier(from)} = ?`).join(' AND ');
+                database.prepare(`DELETE FROM ${quoteSqlIdentifier(table)} WHERE ${predicate}`).run(...parameters);
+            }
+        }
+    }
+}
+function removeInvalidStoredMemoryForMigration(database, invalidEntries) {
+    if (invalidEntries.length === 0)
+        return 0;
+    deleteForeignKeyReferences(database, invalidEntries);
+    const deleteEntry = database.prepare('DELETE FROM entries WHERE id = ? AND workspace = ?');
+    for (const entry of invalidEntries) {
+        const id = recoveryEntryId(entry);
+        if (typeof entry.workspace !== 'string')
+            storedIntegrity();
+        deleteEntry.run(id, entry.workspace);
+    }
+    return invalidEntries.length;
+}
 function migratableRevision(database, row) {
     const entryId = storedNonEmptyString(row.entry_id);
     const createdBy = storedNonEmptyString(row.created_by);
@@ -402,7 +514,7 @@ function migratableRevision(database, row) {
  * the migration transaction; any invalid preimage or canonical collision
  * aborts the whole schema upgrade.
  */
-export function canonicalizeEntryRevisionHashesInMigration(database) {
+export function canonicalizeEntryRevisionHashesInMigration(database, options = {}) {
     const formatTable = database.prepare(`
     SELECT type
       FROM sqlite_schema
@@ -428,14 +540,35 @@ export function canonicalizeEntryRevisionHashesInMigration(database) {
   `).all();
     const entries = database.prepare('SELECT id, workspace FROM entries ORDER BY id')
         .all();
+    const invalidEntries = [];
     for (const entry of entries) {
-        const entryId = storedNonEmptyString(entry.id);
-        const workspace = storedNonEmptyString(entry.workspace);
-        const owner = ownerRevisionChain(database, entryId);
-        if (owner === undefined || owner.workspace !== workspace || !completeRevisionChain(owner))
-            storedIntegrity();
+        try {
+            const entryId = storedNonEmptyString(entry.id);
+            const workspace = storedNonEmptyString(entry.workspace);
+            const owner = ownerRevisionChain(database, entryId);
+            if (owner === undefined || owner.workspace !== workspace || !completeRevisionChain(owner))
+                storedIntegrity();
+            for (const row of rows.filter((candidate) => candidate.entry_id === entryId))
+                migratableRevision(database, row);
+        }
+        catch (error) {
+            if (options.recoverInvalidStoredMemory
+                && error instanceof KiokukoError
+                && error.code === 'INTEGRITY_ERROR'
+                && error.message.startsWith('Stored entry or revision is invalid.')) {
+                invalidEntries.push(entry);
+                continue;
+            }
+            throw error;
+        }
     }
-    const updates = rows.map((row) => migratableRevision(database, row));
+    const recoveredEntries = removeInvalidStoredMemoryForMigration(database, invalidEntries);
+    const updates = database.prepare(`
+    SELECT entry_id, workspace, revision, kind, title, body, summary,
+           scope_json, provenance_json, content_hash, created_by, created_at
+      FROM entry_revisions
+     ORDER BY entry_id, revision
+  `).all().map((row) => migratableRevision(database, row));
     const canonicalIdentities = new Set();
     for (const update of updates) {
         const identity = `${update.workspace}\u0000${update.canonicalHash}`;
@@ -473,7 +606,7 @@ export function canonicalizeEntryRevisionHashesInMigration(database) {
     }
     database.prepare('INSERT INTO entry_revision_hash_format (singleton, algorithm) VALUES (1, ?)')
         .run(REVISION_HASH_ALGORITHM);
-    return { inspected: updates.length, rewritten: changed.length };
+    return { inspected: updates.length, rewritten: changed.length, recoveredEntries };
 }
 function tagsFor(database, entryId, revision) {
     return database

package/dist/memory/revisions.js.map

@@ -1 +1 @@
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package/dist/setup/claude-config.d.ts

@@ -1,4 +1,6 @@
 import type { SkillDiscoveryMode } from '../skills/types.js';
 import type { DelimitedBlockResult } from './managed-text.js';
-export declare function renderClaudeConfig(existing: string | undefined, command?: string, skillDiscoveryMode?: SkillDiscoveryMode): DelimitedBlockResult;
+export declare function renderClaudeConfig(existing: string | undefined, command?: string, skillDiscoveryMode?: SkillDiscoveryMode, options?: {
+    replaceConflictingIdentity?: boolean;
+}): DelimitedBlockResult;
 //# sourceMappingURL=claude-config.d.ts.map

package/dist/setup/claude-config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"claude-config.d.ts","sourceRoot":"","sources":["../../src/setup/claude-config.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAC;AAqC9D,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAAE,OAAO,SAAY,EAAE,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,oBAAoB,CAuCnJ"}
+{"version":3,"file":"claude-config.d.ts","sourceRoot":"","sources":["../../src/setup/claude-config.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAC;AAsC9D,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAC5B,OAAO,SAAY,EACnB,kBAAkB,CAAC,EAAE,kBAAkB,EACvC,OAAO,GAAE;IAAE,0BAA0B,CAAC,EAAE,OAAO,CAAA;CAAO,GACrD,oBAAoB,CA8CtB"}

package/dist/setup/claude-config.js

@@ -1,6 +1,7 @@
 import { applyEdits, modify, parse } from 'jsonc-parser';
 import { KiokukoError } from '../errors.js';
 import { isSkillDiscoveryMode, SKILL_DISCOVERY_ENV } from '../skills/config.js';
+import { setupMcpIdentityConflict } from './mcp-conflict.js';
 import { assertStrictJsonSyntax } from './strict-json.js';
 function object(value) {
     return typeof value === 'object' && value !== null && !Array.isArray(value)
@@ -31,14 +32,18 @@ function validation(message) {
     throw new KiokukoError('VALIDATION_ERROR', message);
 }
 function conflict() {
-    throw new KiokukoError('CONFLICT', 'Claude user config already contains a conflicting kiokuko MCP server');
+    setupMcpIdentityConflict('claude', 'Claude user config already contains a conflicting kiokuko MCP server');
 }
-export function renderClaudeConfig(existing, command = 'kiokuko', skillDiscoveryMode) {
+export function renderClaudeConfig(existing, command = 'kiokuko', skillDiscoveryMode, options = {}) {
     if (!isNonEmptyCommand(command))
         validation('Claude MCP command must be a non-empty executable path or name');
     if (skillDiscoveryMode !== undefined && !isSkillDiscoveryMode(skillDiscoveryMode)) {
         validation('Claude Skill discovery mode is invalid');
     }
+    if (options.replaceConflictingIdentity !== undefined
+        && typeof options.replaceConflictingIdentity !== 'boolean') {
+        validation('Claude MCP replacement authorization is invalid');
+    }
     const source = existing ?? '{}\n';
     assertStrictJsonSyntax(source, { allowTrailingComma: false, disallowComments: true }, 'Claude user config is not a valid JSON object with unique keys');
     const errors = [];
@@ -51,9 +56,12 @@ export function renderClaudeConfig(existing, command = 'kiokuko', skillDiscovery
     if (root.mcpServers !== undefined && mcpServers === undefined)
         validation('Claude user config has an invalid mcpServers object');
     const currentServer = mcpServers?.kiokuko;
-    if (currentServer !== undefined && !isCanonicalManagedServer(currentServer))
+    const canonicalServer = currentServer !== undefined && isCanonicalManagedServer(currentServer)
+        ? currentServer
+        : undefined;
+    if (currentServer !== undefined && canonicalServer === undefined && !options.replaceConflictingIdentity)
         conflict();
-    const currentEnvironment = currentServer === undefined ? undefined : object(currentServer.env);
+    const currentEnvironment = canonicalServer === undefined ? undefined : object(canonicalServer.env);
     const effectiveSkillDiscoveryMode = skillDiscoveryMode
         ?? currentEnvironment?.[SKILL_DISCOVERY_ENV]
         ?? 'official';

package/dist/setup/claude-config.js.map

@@ -1 +1 @@
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package/dist/setup/hermes-config.d.ts

@@ -1,5 +1,7 @@
 import type { SkillDiscoveryMode } from '../skills/types.js';
 import type { DelimitedBlockResult } from './managed-text.js';
 export declare const HERMES_MANAGED_MARKER = "Managed by `kiokuko setup`.";
-export declare function renderHermesConfig(existing: string | undefined, command?: string, skillDiscoveryMode?: SkillDiscoveryMode): DelimitedBlockResult;
+export declare function renderHermesConfig(existing: string | undefined, command?: string, skillDiscoveryMode?: SkillDiscoveryMode, options?: {
+    replaceConflictingIdentity?: boolean;
+}): DelimitedBlockResult;
 //# sourceMappingURL=hermes-config.d.ts.map

package/dist/setup/hermes-config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hermes-config.d.ts","sourceRoot":"","sources":["../../src/setup/hermes-config.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAC;AAG9D,eAAO,MAAM,qBAAqB,gCAAgC,CAAC;AAiGnE,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAC5B,OAAO,SAAY,EACnB,kBAAkB,CAAC,EAAE,kBAAkB,EACvC,OAAO,GAAE;IAAE,0BAA0B,CAAC,EAAE,OAAO,CAAA;CAAO,GACrD,oBAAoB,CA4DtB"}

package/dist/setup/hermes-config.js

@@ -1,6 +1,7 @@
 import { parseDocument, isMap, isNode, isPair, isScalar, isSeq } from 'yaml';
 import { KiokukoError } from '../errors.js';
 import { isSkillDiscoveryMode, SKILL_DISCOVERY_ENV } from '../skills/config.js';
+import { setupMcpIdentityConflict } from './mcp-conflict.js';
 export const HERMES_MANAGED_MARKER = 'Managed by `kiokuko setup`.';
 function scalarValue(value) {
     return isScalar(value) ? value.value : undefined;
@@ -62,7 +63,18 @@ function validation() {
     throw new KiokukoError('VALIDATION_ERROR', 'Hermes config is not a valid YAML mapping');
 }
 function conflict() {
-    throw new KiokukoError('CONFLICT', 'Hermes config already contains a conflicting kiokuko MCP server');
+    setupMcpIdentityConflict('hermes', 'Hermes config already contains a conflicting kiokuko MCP server');
+}
+function managedHermesServerValue(document, command, skillDiscoveryMode) {
+    const value = document.createNode({
+        command,
+        args: ['mcp'],
+        env: { [SKILL_DISCOVERY_ENV]: skillDiscoveryMode },
+    });
+    if (!isNode(value))
+        validation();
+    value.commentBefore = ` ${HERMES_MANAGED_MARKER}`;
+    return value;
 }
 function serializeHermesDocument(document, source, existing) {
     const eol = source.includes('\r\n') ? '\r\n' : '\n';
@@ -73,13 +85,17 @@ function serializeHermesDocument(document, source, existing) {
         action: existing === undefined ? 'created' : content === existing ? 'unchanged' : 'updated',
     };
 }
-export function renderHermesConfig(existing, command = 'kiokuko', skillDiscoveryMode) {
+export function renderHermesConfig(existing, command = 'kiokuko', skillDiscoveryMode, options = {}) {
     if (typeof command !== 'string' || command.trim().length === 0 || command.includes('\0')) {
         throw new KiokukoError('VALIDATION_ERROR', 'Hermes MCP command must be a non-empty executable path or name');
     }
     if (skillDiscoveryMode !== undefined && !isSkillDiscoveryMode(skillDiscoveryMode)) {
         throw new KiokukoError('VALIDATION_ERROR', 'Hermes Skill discovery mode is invalid');
     }
+    if (options.replaceConflictingIdentity !== undefined
+        && typeof options.replaceConflictingIdentity !== 'boolean') {
+        throw new KiokukoError('VALIDATION_ERROR', 'Hermes MCP replacement authorization is invalid');
+    }
     const source = existing ?? '';
     const document = parseDocument(source);
     if (document.errors.length > 0)
@@ -103,8 +119,12 @@ export function renderHermesConfig(existing, command = 'kiokuko', skillDiscovery
     const serverMap = mcpServers;
     const existingPair = findKeyPair(serverMap, 'kiokuko');
     if (existingPair !== undefined) {
-        if (!hasManagedMarker(existingPair) || !hasCanonicalManagedShape(existingPair))
-            conflict();
+        if (!hasManagedMarker(existingPair) || !hasCanonicalManagedShape(existingPair)) {
+            if (!options.replaceConflictingIdentity)
+                conflict();
+            existingPair.value = managedHermesServerValue(document, command, skillDiscoveryMode ?? 'official');
+            return serializeHermesDocument(document, source, existing);
+        }
         const currentSkillDiscoveryMode = currentManagedSkillDiscoveryMode(existingPair);
         if (currentSkillDiscoveryMode === undefined)
             conflict();
@@ -118,14 +138,7 @@ export function renderHermesConfig(existing, command = 'kiokuko', skillDiscovery
         return serializeHermesDocument(document, source, existing);
     }
     const effectiveSkillDiscoveryMode = skillDiscoveryMode ?? 'official';
-    const pair = document.createPair('kiokuko', {
-        command,
-        args: ['mcp'],
-        env: { [SKILL_DISCOVERY_ENV]: effectiveSkillDiscoveryMode },
-    });
-    if (!isNode(pair.value))
-        validation();
-    pair.value.commentBefore = ` ${HERMES_MANAGED_MARKER}`;
+    const pair = document.createPair('kiokuko', managedHermesServerValue(document, command, effectiveSkillDiscoveryMode));
     serverMap.add(pair);
     return serializeHermesDocument(document, source, existing);
 }