fix: coerce non-numeric strings in DB columns during manifest serialization (#2962) (#3229)

SQLite can store string placeholders like "-", "N/A", or "" in INTEGER
columns after schema migrations or manual inserts. snapshotState() was
passing these through as-is via type assertions, producing JSON that
fails to parse on round-trip. Add toNumeric() helper and apply it to
all numeric columns (exit_code, duration_ms, sequence, seq).

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

src/resources/extensions/gsd/tests/workflow-manifest.test.ts

@@ -12,6 +12,7 @@ import {
   insertMilestone,
   insertSlice,
   insertTask,
+  _getAdapter,
 } from '../gsd-db.ts';
 import {
   writeManifest,
@@ -165,6 +166,97 @@ test('workflow-manifest: bootstrapFromManifest restores DB from manifest (round-
   }
 });
 
+// ─── snapshotState: numeric column coercion (#2962) ─────────────────────
+
+test('workflow-manifest: snapshotState coerces string placeholders in numeric columns to null (#2962)', () => {
+  const base = tempDir();
+  openDatabase(tempDbPath(base));
+  try {
+    // Set up prerequisite rows
+    insertMilestone({ id: 'M001' });
+    insertSlice({ id: 'S01', milestoneId: 'M001' });
+    insertTask({ id: 'T01', sliceId: 'S01', milestoneId: 'M001', title: 'Task', status: 'complete' });
+
+    // Insert verification_evidence with string placeholders in numeric columns
+    // This simulates what happens after schema migrations or manual inserts
+    const db = _getAdapter()!;
+    db.prepare(
+      `INSERT INTO verification_evidence (task_id, slice_id, milestone_id, command, exit_code, verdict, duration_ms, created_at)
+       VALUES (?, ?, ?, ?, ?, ?, ?, ?)`,
+    ).run('T01', 'S01', 'M001', 'npm test', '-', 'pass', '-', new Date().toISOString());
+
+    // snapshotState should coerce "-" to null for numeric columns
+    const snap = snapshotState();
+    const ev = snap.verification_evidence[0];
+    assert.strictEqual(ev.exit_code, null, 'exit_code "-" should be coerced to null');
+    assert.strictEqual(ev.duration_ms, null, 'duration_ms "-" should be coerced to null');
+
+    // Round-trip through JSON should not throw
+    const json = JSON.stringify(snap, null, 2);
+    const reparsed = JSON.parse(json);
+    assert.strictEqual(reparsed.verification_evidence[0].exit_code, null);
+    assert.strictEqual(reparsed.verification_evidence[0].duration_ms, null);
+  } finally {
+    closeDatabase();
+    cleanupDir(base);
+  }
+});
+
+test('workflow-manifest: snapshotState coerces empty string and N/A in numeric columns (#2962)', () => {
+  const base = tempDir();
+  openDatabase(tempDbPath(base));
+  try {
+    insertMilestone({ id: 'M001' });
+    insertSlice({ id: 'S01', milestoneId: 'M001' });
+    insertTask({ id: 'T01', sliceId: 'S01', milestoneId: 'M001', title: 'Task', status: 'complete' });
+
+    const db = _getAdapter()!;
+    db.prepare(
+      `INSERT INTO verification_evidence (task_id, slice_id, milestone_id, command, exit_code, verdict, duration_ms, created_at)
+       VALUES (?, ?, ?, ?, ?, ?, ?, ?)`,
+    ).run('T01', 'S01', 'M001', 'npm test', 'N/A', 'pass', '', new Date().toISOString());
+
+    const snap = snapshotState();
+    const ev = snap.verification_evidence[0];
+    assert.strictEqual(ev.exit_code, null, 'exit_code "N/A" should be coerced to null');
+    assert.strictEqual(ev.duration_ms, null, 'duration_ms "" should be coerced to null');
+  } finally {
+    closeDatabase();
+    cleanupDir(base);
+  }
+});
+
+test('workflow-manifest: snapshotState coerces string placeholders in sequence columns (#2962)', () => {
+  const base = tempDir();
+  openDatabase(tempDbPath(base));
+  try {
+    insertMilestone({ id: 'M001' });
+
+    // Insert a slice with a string sequence via raw SQL
+    const db = _getAdapter()!;
+    db.prepare(
+      `INSERT INTO slices (milestone_id, id, title, status, risk, depends, demo, created_at, sequence)
+       VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`,
+    ).run('M001', 'S01', 'Test Slice', 'planned', 'low', '[]', '', new Date().toISOString(), '-');
+
+    db.prepare(
+      `INSERT INTO tasks (milestone_id, slice_id, id, title, status, sequence)
+       VALUES (?, ?, ?, ?, ?, ?)`,
+    ).run('M001', 'S01', 'T01', 'Test Task', 'planned', 'N/A');
+
+    const snap = snapshotState();
+    assert.strictEqual(snap.slices[0].sequence, 0, 'slice sequence "-" should be coerced to 0');
+    assert.strictEqual(snap.tasks[0].sequence, 0, 'task sequence "N/A" should be coerced to 0');
+
+    // JSON round-trip must not throw
+    const json = JSON.stringify(snap, null, 2);
+    assert.doesNotThrow(() => JSON.parse(json));
+  } finally {
+    closeDatabase();
+    cleanupDir(base);
+  }
+});
+
 // ─── readManifest: version check ─────────────────────────────────────────
 
 test('workflow-manifest: readManifest throws on unsupported version', () => {

src/resources/extensions/gsd/workflow-manifest.ts

@@ -42,6 +42,23 @@ function requireDb() {
   return db;
 }
 
+/**
+ * Coerce a raw DB value to a number, returning `fallback` for
+ * null/undefined/non-numeric strings (e.g. "-", "N/A", "").
+ * SQLite can store TEXT in INTEGER columns after migrations or manual inserts.
+ */
+export function toNumeric(value: unknown, fallback: number | null = null): number | null {
+  if (value === null || value === undefined) return fallback;
+  if (typeof value === "number") return Number.isFinite(value) ? value : fallback;
+  if (typeof value === "string") {
+    const trimmed = value.trim();
+    if (trimmed === "" || trimmed === "-" || trimmed === "N/A") return fallback;
+    const n = Number(trimmed);
+    return Number.isFinite(n) ? n : fallback;
+  }
+  return fallback;
+}
+
 // ─── snapshotState ───────────────────────────────────────────────────────
 
 /**
@@ -99,7 +116,7 @@ export function snapshotState(): StateManifest {
     proof_level: (r["proof_level"] as string) ?? "",
     integration_closure: (r["integration_closure"] as string) ?? "",
     observability_impact: (r["observability_impact"] as string) ?? "",
-    sequence: (r["sequence"] as number) ?? 0,
+    sequence: toNumeric(r["sequence"], 0) as number,
     replan_triggered_at: (r["replan_triggered_at"] as string) ?? null,
   }));
 
@@ -129,12 +146,12 @@ export function snapshotState(): StateManifest {
     expected_output: JSON.parse((r["expected_output"] as string) || "[]"),
     observability_impact: (r["observability_impact"] as string) ?? "",
     full_plan_md: (r["full_plan_md"] as string) ?? "",
-    sequence: (r["sequence"] as number) ?? 0,
+    sequence: toNumeric(r["sequence"], 0) as number,
   }));
 
   const rawDecisions = db.prepare("SELECT * FROM decisions ORDER BY seq").all() as Record<string, unknown>[];
   const decisions: Decision[] = rawDecisions.map((r) => ({
-    seq: r["seq"] as number,
+    seq: toNumeric(r["seq"], 0) as number,
     id: r["id"] as string,
     when_context: (r["when_context"] as string) ?? "",
     scope: (r["scope"] as string) ?? "",
@@ -153,9 +170,9 @@ export function snapshotState(): StateManifest {
     slice_id: r["slice_id"] as string,
     milestone_id: r["milestone_id"] as string,
     command: r["command"] as string,
-    exit_code: (r["exit_code"] as number) ?? null,
+    exit_code: toNumeric(r["exit_code"]),
     verdict: (r["verdict"] as string) ?? "",
-    duration_ms: (r["duration_ms"] as number) ?? null,
+    duration_ms: toNumeric(r["duration_ms"]),
     created_at: r["created_at"] as string,
   }));