@cleocode/core 2026.4.30 → 2026.4.35

package/migrations/drizzle-brain/20260411000001_t528-graph-schema-expansion/migration.sql

@@ -0,0 +1,47 @@
+-- T528: Graph-native memory model — expand brain_page_nodes and brain_page_edges schemas.
+-- Adds quality scoring, content hashing, last-activity tracking, provenance, and new
+-- indexes to support traversable knowledge graph operations.
+--
+-- Additive only: all new columns have defaults so existing rows are unaffected.
+-- brain_page_nodes has 0 rows and brain_page_edges has 0 rows (confirmed by R1 audit),
+-- so no data migration is required.
+
+ALTER TABLE `brain_page_nodes` ADD COLUMN `quality_score` real NOT NULL DEFAULT 0.5;
+--> statement-breakpoint
+ALTER TABLE `brain_page_nodes` ADD COLUMN `content_hash` text;
+--> statement-breakpoint
+ALTER TABLE `brain_page_nodes` ADD COLUMN `last_activity_at` text NOT NULL DEFAULT (datetime('now'));
+--> statement-breakpoint
+ALTER TABLE `brain_page_nodes` ADD COLUMN `updated_at` text;
+--> statement-breakpoint
+ALTER TABLE `brain_page_edges` ADD COLUMN `provenance` text;
+--> statement-breakpoint
+
+-- brain_page_edges.weight was nullable (DEFAULT 1) in the initial schema;
+-- changing NOT NULL constraint requires recreating the table in SQLite.
+-- Since brain_page_edges has 0 rows, we drop and recreate.
+DROP TABLE IF EXISTS `brain_page_edges`;
+--> statement-breakpoint
+CREATE TABLE `brain_page_edges` (
+	`from_id` text NOT NULL,
+	`to_id` text NOT NULL,
+	`edge_type` text NOT NULL,
+	`weight` real NOT NULL DEFAULT 1,
+	`provenance` text,
+	`created_at` text NOT NULL DEFAULT (datetime('now')),
+	CONSTRAINT `brain_page_edges_pk` PRIMARY KEY(`from_id`, `to_id`, `edge_type`)
+);
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_brain_nodes_quality` ON `brain_page_nodes` (`quality_score`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_nodes_content_hash` ON `brain_page_nodes` (`content_hash`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_nodes_last_activity` ON `brain_page_nodes` (`last_activity_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_edges_type` ON `brain_page_edges` (`edge_type`);
+--> statement-breakpoint
+-- Re-create existing edge indexes (dropped with table)
+CREATE INDEX IF NOT EXISTS `idx_brain_edges_from` ON `brain_page_edges` (`from_id`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_edges_to` ON `brain_page_edges` (`to_id`);

package/migrations/drizzle-brain/20260412000001_t531-quality-score-typed-tables/migration.sql

@@ -0,0 +1,23 @@
+-- T531: Wire quality scoring into brain memory store functions.
+-- Adds quality_score column to the four typed brain tables.
+-- NULL is used for legacy rows (not yet scored); new rows get a computed score.
+-- Search filtering uses "IS NULL OR quality_score >= 0.3" so legacy entries are retained.
+--
+-- Additive only: all columns are nullable so existing rows are unaffected.
+
+ALTER TABLE `brain_decisions` ADD COLUMN `quality_score` real;
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `quality_score` real;
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `quality_score` real;
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `quality_score` real;
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_brain_decisions_quality` ON `brain_decisions` (`quality_score`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_patterns_quality` ON `brain_patterns` (`quality_score`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_quality` ON `brain_learnings` (`quality_score`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_quality` ON `brain_observations` (`quality_score`);

package/migrations/drizzle-brain/20260413000001_t549-tiered-typed-memory/migration.sql

@@ -0,0 +1,195 @@
+-- T549: Tiered + Typed Memory Architecture v2
+-- Adds: memory_tier, memory_type (cognitive), verified, valid_at, invalid_at,
+--       source_confidence, citation_count to all four typed brain tables.
+--
+-- Strategy: all columns are nullable or have defaults; no existing rows are broken.
+-- NULL-handling contracts: legacy rows are backfilled at the end of this migration.
+-- memory_tier NULL → treated as 'medium' at query time (survived T523 purge).
+-- memory_type NULL → treated as table default at query time.
+-- CONFLICT-03 resolution: citation_count added per cross-validation report (T549-XV).
+-- CONFLICT-01 resolution: cognitive type enum is BRAIN_COGNITIVE_TYPES (semantic/episodic/procedural).
+-- T553 fix: valid_at columns use nullable DEFAULT (datetime('now')) instead of NOT NULL DEFAULT
+--   because SQLite forbids ALTER TABLE ADD COLUMN with a non-constant default on non-empty tables.
+--   The backfill UPDATEs at the end of this migration set valid_at = created_at for all existing
+--   rows, so no row ever has a NULL valid_at after migration completes.
+
+-- ============================================================
+-- brain_decisions
+-- ============================================================
+
+ALTER TABLE `brain_decisions` ADD COLUMN `memory_tier` text DEFAULT 'short';
+--> statement-breakpoint
+ALTER TABLE `brain_decisions` ADD COLUMN `memory_type` text DEFAULT 'semantic';
+--> statement-breakpoint
+ALTER TABLE `brain_decisions` ADD COLUMN `verified` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+ALTER TABLE `brain_decisions` ADD COLUMN `valid_at` text DEFAULT (datetime('now'));
+--> statement-breakpoint
+ALTER TABLE `brain_decisions` ADD COLUMN `invalid_at` text;
+--> statement-breakpoint
+ALTER TABLE `brain_decisions` ADD COLUMN `source_confidence` text DEFAULT 'agent';
+--> statement-breakpoint
+ALTER TABLE `brain_decisions` ADD COLUMN `citation_count` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+
+-- ============================================================
+-- brain_patterns
+-- ============================================================
+
+ALTER TABLE `brain_patterns` ADD COLUMN `memory_tier` text DEFAULT 'short';
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `memory_type` text DEFAULT 'procedural';
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `verified` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `valid_at` text DEFAULT (datetime('now'));
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `invalid_at` text;
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `source_confidence` text DEFAULT 'agent';
+--> statement-breakpoint
+ALTER TABLE `brain_patterns` ADD COLUMN `citation_count` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+
+-- ============================================================
+-- brain_learnings
+-- ============================================================
+
+ALTER TABLE `brain_learnings` ADD COLUMN `memory_tier` text DEFAULT 'short';
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `memory_type` text DEFAULT 'semantic';
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `verified` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `valid_at` text DEFAULT (datetime('now'));
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `invalid_at` text;
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `source_confidence` text DEFAULT 'agent';
+--> statement-breakpoint
+ALTER TABLE `brain_learnings` ADD COLUMN `citation_count` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+
+-- ============================================================
+-- brain_observations
+-- ============================================================
+
+ALTER TABLE `brain_observations` ADD COLUMN `memory_tier` text DEFAULT 'short';
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `memory_type` text DEFAULT 'episodic';
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `verified` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `valid_at` text DEFAULT (datetime('now'));
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `invalid_at` text;
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `source_confidence` text DEFAULT 'agent';
+--> statement-breakpoint
+ALTER TABLE `brain_observations` ADD COLUMN `citation_count` integer NOT NULL DEFAULT 0;
+--> statement-breakpoint
+
+-- ============================================================
+-- Indexes for new columns (query hot paths)
+-- ============================================================
+
+CREATE INDEX IF NOT EXISTS `idx_brain_decisions_tier` ON `brain_decisions` (`memory_tier`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_decisions_type` ON `brain_decisions` (`memory_type`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_decisions_verified` ON `brain_decisions` (`verified`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_decisions_valid_at` ON `brain_decisions` (`valid_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_decisions_source_conf` ON `brain_decisions` (`source_confidence`);
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_brain_patterns_tier` ON `brain_patterns` (`memory_tier`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_patterns_type` ON `brain_patterns` (`memory_type`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_patterns_verified` ON `brain_patterns` (`verified`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_patterns_valid_at` ON `brain_patterns` (`valid_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_patterns_source_conf` ON `brain_patterns` (`source_confidence`);
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_tier` ON `brain_learnings` (`memory_tier`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_type` ON `brain_learnings` (`memory_type`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_verified` ON `brain_learnings` (`verified`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_valid_at` ON `brain_learnings` (`valid_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_invalid` ON `brain_learnings` (`invalid_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_learnings_source_conf` ON `brain_learnings` (`source_confidence`);
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_tier` ON `brain_observations` (`memory_tier`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_type` ON `brain_observations` (`memory_type`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_verified` ON `brain_observations` (`verified`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_valid_at` ON `brain_observations` (`valid_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_invalid` ON `brain_observations` (`invalid_at`);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_brain_observations_source_conf` ON `brain_observations` (`source_confidence`);
+--> statement-breakpoint
+
+-- ============================================================
+-- Backfill: legacy rows (survivors of the T523 purge)
+-- Treat existing rows as medium-to-long-term based on quality signals.
+-- valid_at defaults to created_at so bitemporal queries work correctly.
+-- ============================================================
+
+UPDATE `brain_decisions` SET
+  memory_tier = CASE
+    WHEN confidence = 'high' THEN 'long'
+    WHEN confidence = 'medium' THEN 'medium'
+    ELSE 'medium'
+  END,
+  memory_type = 'semantic',
+  valid_at = created_at,
+  source_confidence = 'agent'
+WHERE memory_tier IS NULL;
+--> statement-breakpoint
+
+UPDATE `brain_patterns` SET
+  memory_tier = CASE
+    WHEN frequency >= 5 THEN 'long'
+    WHEN frequency >= 2 THEN 'medium'
+    ELSE 'medium'
+  END,
+  memory_type = 'procedural',
+  valid_at = extracted_at,
+  source_confidence = 'agent'
+WHERE memory_tier IS NULL;
+--> statement-breakpoint
+
+UPDATE `brain_learnings` SET
+  memory_tier = CASE
+    WHEN confidence >= 0.80 THEN 'long'
+    WHEN confidence >= 0.60 THEN 'medium'
+    ELSE 'medium'
+  END,
+  memory_type = 'semantic',
+  valid_at = created_at,
+  source_confidence = 'agent'
+WHERE memory_tier IS NULL;
+--> statement-breakpoint
+
+UPDATE `brain_observations` SET
+  memory_tier = 'medium',
+  memory_type = 'episodic',
+  valid_at = created_at,
+  source_confidence = CASE
+    WHEN source_type = 'manual' THEN 'owner'
+    WHEN source_type = 'session-debrief' THEN 'task-outcome'
+    ELSE 'agent'
+  END
+WHERE memory_tier IS NULL;

package/migrations/drizzle-nexus/20260412000001_t529-nexus-graph-tables/migration.sql

@@ -0,0 +1,49 @@
+CREATE TABLE IF NOT EXISTS `nexus_nodes` (
+	`id` text PRIMARY KEY,
+	`project_id` text NOT NULL,
+	`kind` text NOT NULL,
+	`label` text NOT NULL,
+	`name` text,
+	`file_path` text,
+	`start_line` integer,
+	`end_line` integer,
+	`language` text,
+	`is_exported` integer DEFAULT false NOT NULL,
+	`parent_id` text,
+	`parameters_json` text,
+	`return_type` text,
+	`doc_summary` text,
+	`community_id` text,
+	`meta_json` text,
+	`indexed_at` text DEFAULT (datetime('now')) NOT NULL
+);
+--> statement-breakpoint
+CREATE TABLE IF NOT EXISTS `nexus_relations` (
+	`id` text PRIMARY KEY,
+	`project_id` text NOT NULL,
+	`source_id` text NOT NULL,
+	`target_id` text NOT NULL,
+	`type` text NOT NULL,
+	`confidence` real NOT NULL,
+	`reason` text,
+	`step` integer,
+	`indexed_at` text DEFAULT (datetime('now')) NOT NULL
+);
+--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_project` ON `nexus_nodes` (`project_id`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_kind` ON `nexus_nodes` (`kind`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_file` ON `nexus_nodes` (`file_path`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_name` ON `nexus_nodes` (`name`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_project_kind` ON `nexus_nodes` (`project_id`,`kind`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_project_file` ON `nexus_nodes` (`project_id`,`file_path`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_community` ON `nexus_nodes` (`community_id`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_parent` ON `nexus_nodes` (`parent_id`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_nodes_exported` ON `nexus_nodes` (`is_exported`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_project` ON `nexus_relations` (`project_id`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_source` ON `nexus_relations` (`source_id`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_target` ON `nexus_relations` (`target_id`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_type` ON `nexus_relations` (`type`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_project_type` ON `nexus_relations` (`project_id`,`type`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_source_type` ON `nexus_relations` (`source_id`,`type`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_target_type` ON `nexus_relations` (`target_id`,`type`);--> statement-breakpoint
+CREATE INDEX IF NOT EXISTS `idx_nexus_relations_confidence` ON `nexus_relations` (`confidence`);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cleocode/core",
-  "version": "2026.4.30",
+  "version": "2026.4.35",
   "description": "CLEO core business logic kernel — tasks, sessions, memory, orchestration, lifecycle, with bundled SQLite store",
   "type": "module",
   "main": "./dist/index.js",
@@ -32,28 +32,28 @@
     "pino": "^10.3.1",
     "pino-roll": "^4.0.0",
     "proper-lockfile": "^4.1.2",
+    "sqlite-vec": "^0.1.9",
     "tar": "^7.4.3",
-    "write-file-atomic": "^7.0.1",
-    "yaml": "^2.8.3",
-    "zod": "^4.3.6",
-    "@cleocode/adapters": "2026.4.30",
-    "@cleocode/caamp": "2026.4.30",
-    "@cleocode/contracts": "2026.4.30",
-    "@cleocode/lafs": "2026.4.30",
-    "@cleocode/agents": "2026.4.30",
-    "@cleocode/skills": "2026.4.30"
-  },
-  "optionalDependencies": {
-    "tree-sitter-c": "^0.24.1",
-    "tree-sitter-cli": "^0.26.7",
+    "tree-sitter": "^0.22.1",
+    "tree-sitter-c": "^0.23.2",
     "tree-sitter-cpp": "^0.23.4",
-    "tree-sitter-go": "^0.25.0",
+    "tree-sitter-go": "^0.23.0",
     "tree-sitter-java": "^0.23.5",
-    "tree-sitter-javascript": "^0.25.0",
-    "tree-sitter-python": "^0.25.0",
+    "tree-sitter-javascript": "^0.23.0",
+    "tree-sitter-python": "^0.23.4",
     "tree-sitter-ruby": "^0.23.1",
-    "tree-sitter-rust": "^0.24.0",
-    "tree-sitter-typescript": "^0.23.2"
+    "tree-sitter-rust": "^0.23.1",
+    "tree-sitter-typescript": "^0.23.2",
+    "write-file-atomic": "^7.0.1",
+    "yaml": "^2.8.3",
+    "zod": "^4.3.6",
+    "@cleocode/adapters": "2026.4.35",
+    "@cleocode/agents": "2026.4.35",
+    "@cleocode/caamp": "2026.4.35",
+    "@cleocode/contracts": "2026.4.35",
+    "@cleocode/lafs": "2026.4.35",
+    "@cleocode/nexus": "2026.4.35",
+    "@cleocode/skills": "2026.4.35"
   },
   "engines": {
     "node": ">=24.0.0"

package/src/bootstrap.ts

@@ -379,8 +379,132 @@ async function installProviderAdapters(
 
 // ── Step 7: Post-bootstrap health verification ───────────────────────
 
+/**
+ * Combined bootstrap health + dependency verification result.
+ *
+ * Produced by {@link verifyBootstrapComplete} and intended for consumers
+ * such as `postinstall.js` and `cleo install-global` that need a single
+ * aggregated view of system readiness after bootstrap completes.
+ */
+export interface BootstrapVerificationResult {
+  /** `true` when both bootstrap injection-chain health and all required dependencies are healthy. */
+  complete: boolean;
+  /** `true` when the injection-chain health checks (template files, AGENTS.md) all pass. */
+  bootstrapHealthy: boolean;
+  /** `true` when every `required` dependency is healthy (see {@link DependencyReport.allRequiredMet}). */
+  dependenciesHealthy: boolean;
+  /** Human-readable failure descriptions from both the injection-chain and dependency checks. */
+  failures: string[];
+  /** Non-fatal advisory messages (optional deps missing, template version skew, etc.). */
+  warnings: string[];
+}
+
+/**
+ * Run both injection-chain health verification and full dependency checks after bootstrap.
+ *
+ * Combines:
+ *   1. Injection-chain health (XDG template, legacy template version sync, AGENTS.md reference,
+ *      orphaned content detection) — delegated to the internal {@link verifyBootstrapHealth}.
+ *   2. All registered runtime dependencies — delegated to {@link checkAllDependencies} from
+ *      `./system/dependencies.js`.
+ *
+ * This function is intentionally non-throwing. Every error is captured and surfaced through
+ * the returned {@link BootstrapVerificationResult} so callers (postinstall, CLI commands) can
+ * decide how to present failures without crashing the install process.
+ *
+ * @returns A {@link BootstrapVerificationResult} aggregating both checks.
+ */
+export async function verifyBootstrapComplete(): Promise<BootstrapVerificationResult> {
+  const failures: string[] = [];
+  const warnings: string[] = [];
+
+  // ── Part 1: Injection-chain health ──────────────────────────────────────────
+  let bootstrapHealthy = true;
+
+  try {
+    const healthCtx: BootstrapContext = {
+      created: [],
+      warnings: [],
+      isDryRun: false,
+    };
+
+    await verifyBootstrapHealth(healthCtx);
+
+    // verifyBootstrapHealth appends to ctx.warnings on issues — treat all as warnings.
+    // There is no way to distinguish bootstrap-fatal from advisory in the current impl,
+    // so we surface them all as warnings (consistent with the existing non-blocking design).
+    for (const w of healthCtx.warnings) {
+      warnings.push(w);
+    }
+
+    // If any warnings were produced by the health check, mark bootstrap as degraded
+    // but not outright failed (health check is advisory-only by design).
+    if (healthCtx.warnings.length > 0) {
+      bootstrapHealthy = false;
+    }
+  } catch (err) {
+    bootstrapHealthy = false;
+    failures.push(
+      `Bootstrap health check failed: ${err instanceof Error ? err.message : String(err)}`,
+    );
+  }
+
+  // ── Part 2: Dependency checks ────────────────────────────────────────────────
+  let dependenciesHealthy = false;
+
+  try {
+    const { checkAllDependencies } = await import('./system/dependencies.js');
+    const depReport = await checkAllDependencies();
+
+    dependenciesHealthy = depReport.allRequiredMet;
+
+    for (const result of depReport.results) {
+      if (result.category === 'required' && !result.healthy) {
+        const msg = result.error
+          ? `Required dependency '${result.name}' unhealthy: ${result.error}`
+          : `Required dependency '${result.name}' is not healthy`;
+        failures.push(msg);
+      }
+    }
+
+    // Surface dependency warnings (optional / feature deps missing)
+    for (const w of depReport.warnings) {
+      warnings.push(w);
+    }
+  } catch (err) {
+    // Dependency check failure is non-fatal — mark as unknown (default false)
+    warnings.push(`Dependency check deferred: ${err instanceof Error ? err.message : String(err)}`);
+  }
+
+  return {
+    complete: bootstrapHealthy && dependenciesHealthy,
+    bootstrapHealthy,
+    dependenciesHealthy,
+    failures,
+    warnings,
+  };
+}
+
 /**
  * Verify the injection chain is intact after bootstrap.
+ *
+ * This function serves a DIFFERENT purpose than `startupHealthCheck()` in
+ * `packages/core/src/system/health.ts` (T511 — documented separation):
+ *
+ * - `verifyBootstrapHealth()` — checks global CAAMP injection-chain state:
+ *   XDG template existence + version, AGENTS.md reference correctness, and
+ *   orphaned CAAMP block fragments. Called ONLY after `bootstrapGlobalCleo()`
+ *   completes (post-install, self-update). NOT called on every startup.
+ *
+ * - `startupHealthCheck()` — checks project and global *scaffold* health:
+ *   .cleo/ directory structure, tasks.db, config.json, global ~/.cleo/ dirs.
+ *   Called on every CLI startup to detect drift.
+ *
+ * These are complementary, not duplicates. Neither delegates to the other
+ * because their scopes and lifecycles differ:
+ *   - Bootstrap health only makes sense after bootstrap completes.
+ *   - Startup health must be ultra-fast (no CAAMP parsing) and runs unconditionally.
+ *
  * Checks:
  *   1. XDG template exists and has a version header
  *   2. Legacy template (if present) matches XDG version

package/src/code/index.ts

@@ -1,10 +1,26 @@
 /**
  * Code analysis via tree-sitter AST parsing.
  *
+ * @deprecated Import directly from `@cleocode/nexus` instead.
+ *
+ * This barrel is retained for backward compatibility. The canonical
+ * implementation lives in `@cleocode/nexus/src/code/`. Consumers in the
+ * `@cleocode/core` dispatch layer that need these symbols should import
+ * from `@cleocode/nexus` directly.
+ *
  * @module code
  */
 
-export { type OutlineNode, type SmartOutlineResult, smartOutline } from './outline.js';
-export { batchParse, parseFile } from './parser.js';
-export { type SmartSearchOptions, type SmartSearchResult, smartSearch } from './search.js';
-export { type SmartUnfoldResult, smartUnfold } from './unfold.js';
+export {
+  batchParse,
+  isTreeSitterAvailable,
+  type OutlineNode,
+  parseFile,
+  type SmartOutlineResult,
+  type SmartSearchOptions,
+  type SmartSearchResult,
+  type SmartUnfoldResult,
+  smartOutline,
+  smartSearch,
+  smartUnfold,
+} from '@cleocode/nexus';