Merge remote-tracking branch 'origin/master' into session-query-search

# Conflicts:
#	.agents/notes/implemented/feature/2026-07-10-session-query-service.md
#	.agents/notes/implemented/feature/2026-07-10-sqlite-session-query-provider.md
#	.agents/notes/proposed/feature/2026-07-10-sqlite-session-query-provider.md
#	docs/architecture.md
#	docs/capability-seams.md
#	docs/config-catalog.md
#	docs/cordis-catalog/services.md
#	docs/core-data-structures/core.md
#	docs/core-data-structures/persistence.md
#	docs/core-data-structures/session-query.md
#	docs/module-graph.md
#	docs/rfc/INDEX.md
#	packages/README.md
#	packages/cordis/tool-cordis/src/api-catalog.ts
#	packages/hooks/hooks-claude/tests/coverage.spec.ts
#	packages/session-persistence/session-persistence-jsonl/src/index.ts
#	packages/session-persistence/session-persistence-jsonl/tests/jsonl.spec.ts
#	packages/session-persistence/session-persistence-sqlite/README.md
#	packages/session-persistence/session-persistence-sqlite/src/index.ts
#	packages/session-persistence/session-persistence-sqlite/src/schema.ts
#	packages/session-persistence/session-persistence-sqlite/tests/sqlite.spec.ts
#	packages/session-persistence/session-persistence/README.md
#	packages/session-persistence/session-persistence/package.json
#	packages/session-query/README.md
#	packages/session-query/session-query/README.md
#	packages/session-query/session-query/package.json
#	packages/session-query/session-query/src/config.ts
#	packages/session-query/session-query/src/index.ts
#	packages/session-query/session-query/src/types.ts
#	pnpm-lock.yaml
#	scripts/gen-doc-graphs.ts
#	scripts/type-equiv.manifest.json
#	tsconfig.host.json
#	tsconfig.json

packages/session-persistence/session-persistence-sqlite/src/index.ts

@@ -1,7 +1,8 @@
 /**
  * SQLite durable session-persistence backend. It maps each session header and
  * event to rows, and delegates write-path orchestration to
- * {@link PersistenceCoordinator}.
+ * {@link PersistenceCoordinator}. It has no independent per-session artifact,
+ * so its locator returns `undefined`.
  * @module @deepseek-ai/dsh-session-persistence-sqlite
  */
 
@@ -10,11 +11,12 @@ import z from 'schemastery'
 import { randomUUID } from 'node:crypto'
 import { statSync } from 'node:fs'
 import { DatabaseSync } from 'node:sqlite'
-import { mkdir } from 'node:fs/promises'
+import { mkdir, open } from 'node:fs/promises'
 import { dirname, resolve } from 'node:path'
 import {
   SessionPersistence, SessionPersistenceRevision, PersistenceCoordinator,
-  type PersistenceBackend, type SessionPersistenceSnapshot, type StoredPrefix,
+  type PersistenceBackend, type SessionLocation, type SessionPersistenceSnapshot,
+  type StoredPrefix,
 } from '@deepseek-ai/dsh-session-persistence'
 import type { SessionEvent, SurfaceEventType, SessionId, SessionHeader } from '@deepseek-ai/dsh-session'
 import {
@@ -36,12 +38,32 @@ function surfaceBindings(event: SessionEvent): [string | null, string | null] {
   ]
 }
 
+/**
+ * Exclusively create a missing database file with owner-only permissions.
+ * Existing files retain their modes, and errors other than `EEXIST` propagate.
+ * `DatabaseSync` reopens by path, so this does not protect confidentiality or
+ * integrity when another principal can replace the database entry in its parent
+ * directory.
+ */
+async function createDatabaseFile(path: string): Promise<void> {
+  try {
+    const handle = await open(path, 'wx', 0o600)
+    await handle.close()
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code !== 'EEXIST') throw error
+  }
+}
+
 /** Plugin configuration. */
 export interface Config {
   /**
    * Filesystem path to the SQLite database file. The special value `:memory:`
-   * opens an in-process database (tests); a file path is created (with parent
-   * dirs) on construction.
+   * opens an in-process database (tests). On filesystems with POSIX modes,
+   * missing directories and databases are created owner-only; existing path
+   * modes are preserved. Filesystem setup errors other than an existing database
+   * fail initialization. The backend does not protect confidentiality or
+   * integrity when another principal can replace the database entry in its
+   * parent directory.
    */
   path: string
   /**
@@ -88,7 +110,10 @@ export class SessionPersistenceSqlite extends SessionPersistence implements Pers
 
   private async openDb(path: string, journalMode: JournalMode): Promise<void> {
     const actual = path === ':memory:' ? path : resolve(path)
-    if (actual !== ':memory:') await mkdir(dirname(actual), { recursive: true, mode: 0o700 })
+    if (actual !== ':memory:') {
+      await mkdir(dirname(actual), { recursive: true, mode: 0o700 })
+      await createDatabaseFile(actual)
+    }
     this.db = openDatabase(actual, journalMode)
     try {
       const row = this.db.prepare(
@@ -115,6 +140,11 @@ export class SessionPersistenceSqlite extends SessionPersistence implements Pers
 
   // --- SessionPersistence service surface (delegated to the coordinator) ---
 
+  /** SQLite has one database, not an independent local artifact per session. */
+  locate(_meta: SessionHeader): SessionLocation | undefined {
+    return undefined
+  }
+
   create(meta: SessionHeader): Promise<void> {
     return this.coordinator.create(meta)
   }
@@ -263,14 +293,15 @@ export class SessionPersistenceSqlite extends SessionPersistence implements Pers
   private writeRow(meta: SessionHeader): void {
     this.db.prepare(`
       INSERT INTO sessions
-        (id, version, created_at, cwd, parent_session, seed_length, incarnation, revision)
-      VALUES (?, ?, ?, ?, ?, ?, ?, 0)
+        (id, version, created_at, cwd, parent_session, seed_length, delegation_depth, incarnation, revision)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, 0)
       ON CONFLICT(id) DO UPDATE SET
         version = excluded.version,
         created_at = excluded.created_at,
         cwd = excluded.cwd,
         parent_session = excluded.parent_session,
-        seed_length = excluded.seed_length
+        seed_length = excluded.seed_length,
+        delegation_depth = excluded.delegation_depth
     `).run(
       meta.id,
       meta.version,
@@ -278,6 +309,7 @@ export class SessionPersistenceSqlite extends SessionPersistence implements Pers
       meta.cwd ?? null,
       meta.parentSession ?? null,
       meta.seedLength ?? null,
+      meta.delegationDepth ?? null,
       randomUUID(),
     )
   }

packages/session-persistence/session-persistence-sqlite/src/invariant.ts

@@ -0,0 +1,30 @@
+/**
+ * Package-owned invariant companion for `@deepseek-ai/dsh-session-persistence-sqlite`.
+ * @module @deepseek-ai/dsh-session-persistence-sqlite/invariant
+ */
+
+/* jscpd:ignore-start */
+import type { Context } from 'cordis'
+import type { InvariantInstaller } from '@deepseek-ai/dsh-invariants'
+
+const PACKAGE_NAME = '@deepseek-ai/dsh-session-persistence-sqlite'
+
+/** Cordis companion plugin name. */
+export const name = 'session-persistence-sqlite-invariant'
+/** Service required before the companion can reserve package ownership. */
+export const inject = ['invariants']
+
+/**
+ * No runtime invariant: persistence correctness requires backend round-trip and crash-tail tests;
+ * this package exposes no continuously observable in-process relation.
+ */
+const install: InvariantInstaller = () => {}
+
+/**
+ * Register this package's invariant companion.
+ * @param ctx - Cordis context carrying the invariant service.
+ * @returns the installed registration's disposer after setup succeeds.
+ */
+export const apply = (ctx: Context): Promise<() => void> =>
+  Promise.resolve(ctx.invariants.register(PACKAGE_NAME, install))
+/* jscpd:ignore-end */

packages/session-persistence/session-persistence-sqlite/src/schema.ts

@@ -17,7 +17,7 @@ import type { SessionEvent, SessionId, SessionHeader, SurfaceOp } from '@deepsee
  * layout; orthogonal to a session's own `version` (which versions the EVENT
  * vocabulary, stored per session in the `sessions` row).
  */
-export const SCHEMA_VERSION = 7
+export const SCHEMA_VERSION = 8
 
 /**
  * A row of the `sessions` table — the out-of-log metadata ({@link SessionHeader}).
@@ -37,6 +37,7 @@ export interface SessionRow {
   incarnation: string
   /** Monotonic log-change token incremented in each mutating transaction. */
   revision: number
+  delegation_depth: number | null
 }
 
 /** An `events` table row: one `SessionEvent` mapped 1:1 (`data` is JSON text). */
@@ -107,11 +108,12 @@ function configureDatabase(db: DatabaseSync, path: string, journalMode: JournalM
       id             TEXT PRIMARY KEY,
       version        INTEGER NOT NULL,
       created_at     INTEGER NOT NULL,
-      cwd            TEXT,
-      parent_session TEXT,
-      seed_length    INTEGER,
-      incarnation    TEXT NOT NULL,
-      revision       INTEGER NOT NULL
+      cwd              TEXT,
+      parent_session   TEXT,
+      seed_length      INTEGER,
+      delegation_depth INTEGER,
+      incarnation      TEXT NOT NULL,
+      revision         INTEGER NOT NULL
     ) STRICT
   `)
   db.exec(`
@@ -141,6 +143,7 @@ export function rowToMeta(row: SessionRow): SessionHeader {
     ...row.cwd !== null ? { cwd: row.cwd } : {},
     ...row.parent_session !== null ? { parentSession: row.parent_session as SessionId } : {},
     ...row.seed_length !== null ? { seedLength: row.seed_length } : {},
+    ...row.delegation_depth !== null ? { delegationDepth: row.delegation_depth } : {},
   }
 }
 
@@ -188,8 +191,8 @@ export function scanRows(rows: readonly EventRow[]): { preserved: SessionEvent[]
     }
   })
 
-  // The last index that is a valid `turn/end` — the last fully-committed
-  // boundary (the loop flushes only at turn/end).
+  // The last index that is a valid `turn/end` — holes through a closed turn
+  // are always committed corruption.
   let lastTurnEnd = -1
   for (let i = parsed.length - 1; i >= 0; i--) {
     if (parsed[i]?.ok && rows[i]?.type === 'turn/end') { lastTurnEnd = i; break }