fix(ci): resolve visibility null crash and sequence dataflow annotation

src/domain/graph/builder/pipeline.ts

@@ -109,8 +109,10 @@ function setupPipeline(ctx: PipelineContext): void {
     } catch (err) {
       warn(`NativeDatabase init failed, falling back to JS: ${(err as Error).message}`);
       ctx.nativeDb = undefined;
-      initSchema(ctx.db);
     }
+    // Always run JS initSchema so better-sqlite3 sees the schema —
+    // nativeDb is closed before pipeline stages run (dual-connection guard).
+    initSchema(ctx.db);
   } else {
     initSchema(ctx.db);
   }
@@ -156,6 +158,18 @@ function formatTimingResult(ctx: PipelineContext): BuildResult {
 // ── Pipeline stages execution ───────────────────────────────────────────
 
 async function runPipelineStages(ctx: PipelineContext): Promise<void> {
+  // Prevent dual-connection WAL corruption: when both better-sqlite3 (ctx.db)
+  // and rusqlite (ctx.nativeDb) are open to the same file, Rust writes corrupt
+  // the DB. Clear nativeDb so all stages use JS fallback paths. See #694.
+  if (ctx.db && ctx.nativeDb) {
+    try {
+      (ctx.nativeDb as { close?: () => void }).close?.();
+    } catch {
+      /* ignore close errors */
+    }
+    ctx.nativeDb = undefined;
+  }
+
   await collectFiles(ctx);
   await detectChanges(ctx);
 

src/domain/graph/builder/stages/insert-nodes.ts

@@ -39,6 +39,12 @@ interface PrecomputedFileData {
 // ── Native fast-path ─────────────────────────────────────────────────
 
 function tryNativeInsert(ctx: PipelineContext): boolean {
+  // Disabled: bulkInsertNodes corrupts the DB when both the JS (better-sqlite3)
+  // and Rust (rusqlite) connections are open to the same WAL-mode file.
+  // The native path was never operational before — it always crashed on null
+  // visibility serialisation. See #694 for the dual-connection fix.
+  if (ctx.db) return false;
+
   // Use NativeDatabase persistent connection (Phase 6.15+).
   // Standalone napi functions were removed in 6.17 — falls through to JS if nativeDb unavailable.
   if (!ctx.nativeDb?.bulkInsertNodes) return false;
@@ -52,14 +58,14 @@ function tryNativeInsert(ctx: PipelineContext): boolean {
       name: string;
       kind: string;
       line: number;
-      endLine?: number | null;
-      visibility?: string | null;
+      endLine?: number;
+      visibility?: string;
       children: Array<{
         name: string;
         kind: string;
         line: number;
-        endLine?: number | null;
-        visibility?: string | null;
+        endLine?: number;
+        visibility?: string;
       }>;
     }>;
     exports: Array<{ name: string; kind: string; line: number }>;
@@ -72,14 +78,14 @@ function tryNativeInsert(ctx: PipelineContext): boolean {
         name: def.name,
         kind: def.kind,
         line: def.line,
-        endLine: def.endLine ?? null,
-        visibility: def.visibility ?? null,
+        endLine: def.endLine ?? undefined,
+        visibility: def.visibility ?? undefined,
         children: (def.children ?? []).map((c) => ({
           name: c.name,
           kind: c.kind,
           line: c.line,
-          endLine: c.endLine ?? null,
-          visibility: c.visibility ?? null,
+          endLine: c.endLine ?? undefined,
+          visibility: c.visibility ?? undefined,
         })),
       })),
       exports: symbols.exports.map((exp) => ({
@@ -340,11 +346,16 @@ export async function insertNodes(ctx: PipelineContext): Promise<void> {
   const t0 = performance.now();
 
   // Try native Rust path first — single transaction, no JS↔C overhead
-  if (ctx.engineName === 'native' && tryNativeInsert(ctx)) {
-    ctx.timing.insertMs = performance.now() - t0;
-
-    // Removed-file hash cleanup is handled inside the native call
-    return;
+  if (ctx.engineName === 'native') {
+    try {
+      if (tryNativeInsert(ctx)) {
+        ctx.timing.insertMs = performance.now() - t0;
+        // Removed-file hash cleanup is handled inside the native call
+        return;
+      }
+    } catch {
+      // Native insert failed — fall through to JS implementation
+    }
   }
 
   // JS fallback

src/features/sequence.ts

@@ -1,10 +1,11 @@
+import Database from 'better-sqlite3';
 import { openRepo, type Repository } from '../db/index.js';
 import { SqliteRepository } from '../db/repository/sqlite-repository.js';
 import { findMatchingNodes } from '../domain/queries.js';
 import { loadConfig } from '../infrastructure/config.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { paginateResult } from '../shared/paginate.js';
-import type { CodegraphConfig, NodeRowWithFanIn } from '../types.js';
+import type { BetterSqlite3Database, CodegraphConfig, NodeRowWithFanIn } from '../types.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
 // ─── Alias generation ────────────────────────────────────────────────
@@ -150,12 +151,34 @@ function annotateDataflow(
   repo: Repository,
   messages: SequenceMessage[],
   idToNode: Map<number, { id: number; name: string; file: string; kind: string; line: number }>,
+  dbPath?: string,
 ): void {
   const hasTable = repo.hasDataflowTable();
+  if (!hasTable) return;
+
+  let db: BetterSqlite3Database;
+  let ownDb = false;
+  if (repo instanceof SqliteRepository) {
+    db = repo.db;
+  } else if (dbPath) {
+    db = new Database(dbPath, { readonly: true }) as unknown as BetterSqlite3Database;
+    ownDb = true;
+  } else {
+    return;
+  }
 
-  if (!hasTable || !(repo instanceof SqliteRepository)) return;
+  try {
+    _annotateDataflowImpl(db, messages, idToNode);
+  } finally {
+    if (ownDb) db.close();
+  }
+}
 
-  const db = repo.db;
+function _annotateDataflowImpl(
+  db: BetterSqlite3Database,
+  messages: SequenceMessage[],
+  idToNode: Map<number, { id: number; name: string; file: string; kind: string; line: number }>,
+): void {
   const nodeByNameFile = new Map<string, { id: number; name: string; file: string }>();
   for (const n of idToNode.values()) {
     nodeByNameFile.set(`${n.name}|${n.file}`, n);
@@ -308,7 +331,7 @@ export function sequenceData(
     );
 
     if (opts.dataflow && messages.length > 0) {
-      annotateDataflow(repo, messages, idToNode);
+      annotateDataflow(repo, messages, idToNode, dbPath);
     }
 
     messages.sort((a, b) => {