fix: address verified gadfly P5/#5 findings (contrib/store concurrency)

All 3 cloud models converged on real concurrency bugs in the SQLite stores:

- AppendVersion (HIGH): the seq key was `SELECT MAX(seq)+1` then INSERT in two
  un-transacted statements with a NON-unique index, AND the Scan error was
  swallowed (seq stayed 0 on failure). Concurrent appends could both land the
  same seq, silently breaking newest-first ordering. Now: one transaction, the
  Scan error is propagated, the (skill_id, seq) index is UNIQUE (the loser of a
  race fails loudly), and an empty SkillID is rejected.
- MarkScheduledRun / MarkAgentScheduledRun (all 3): replaced the Get→mutate→Save
  read-modify-write (lost-update window) with a single atomic UPDATE using
  json_set, so a concurrent Mark/edit can't clobber it. json_set keeps the JSON
  blob's NextRunAt/LastScheduledRunAt consistent with the indexed column;
  RFC3339Nano matches Go's time encoding so the blob still round-trips (tested).
- Open: actually applies PRAGMA busy_timeout=5000 (the doc advertised it but it
  was never set) — a contended writer waits instead of erroring SQLITE_BUSY.
- budgetStore.Add: rejects NaN/Inf secondsUsed (would irrecoverably poison the
  column).

Triaged-but-kept: plaintext webhook secret (documented design, high-entropy URL
key, pre-existing); SQL()/free-form `where` helpers (no untrusted input reaches
them — defense-in-depth notes only).

Core go.sum still free of host/DB deps; contrib/store green (incl. a json_set
blob-round-trip test).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

contrib/store/skill_store.go

@@ -45,7 +45,7 @@ CREATE TABLE IF NOT EXISTS skill_versions (
 	seq       INTEGER NOT NULL,            -- append order, for newest-first
 	data      TEXT NOT NULL
 );
-CREATE INDEX IF NOT EXISTS idx_skill_versions_skill ON skill_versions(skill_id, seq);`)
+CREATE UNIQUE INDEX IF NOT EXISTS idx_skill_versions_skill ON skill_versions(skill_id, seq);`)
 	if err != nil {
 		return fmt.Errorf("skillStore.Initialize: %w", err)
 	}
@@ -182,27 +182,56 @@ func (s *skillStore) ListDueScheduled(ctx context.Context, now time.Time) ([]ski
 }
 
 func (s *skillStore) MarkScheduledRun(ctx context.Context, skillID string, ranAt, nextAt time.Time) error {
-	sk, err := s.Get(ctx, skillID)
-	if err != nil {
-		return err
+	// Single atomic statement instead of Get→mutate→Save: a concurrent Mark or
+	// admin edit can't lose this update (no read-modify-write window). json_set
+	// keeps the JSON blob's NextRunAt/LastScheduledRunAt consistent with the
+	// indexed next_run_at column; RFC3339Nano matches Go's time JSON encoding so
+	// the blob still round-trips through Get.
+	var next int64
+	if !nextAt.IsZero() {
+		next = nextAt.Unix()
 	}
-	sk.LastScheduledRunAt = ranAt
-	sk.NextRunAt = nextAt
-	return s.Save(ctx, sk)
+	res, err := s.db.ExecContext(ctx,
+		`UPDATE skills SET next_run_at=?, data=json_set(data,'$.NextRunAt',?,'$.LastScheduledRunAt',?) WHERE id=?`,
+		next, nextAt.Format(time.RFC3339Nano), ranAt.Format(time.RFC3339Nano), skillID)
+	if err != nil {
+		return fmt.Errorf("skillStore.MarkScheduledRun: %w", err)
+	}
+	if n, _ := res.RowsAffected(); n == 0 {
+		return skill.ErrNotFound
+	}
+	return nil
 }
 
 func (s *skillStore) AppendVersion(ctx context.Context, sv skill.SkillVersion) error {
+	if sv.SkillID == "" {
+		return fmt.Errorf("skillStore.AppendVersion: skill_id is required")
+	}
 	blob, err := json.Marshal(sv)
 	if err != nil {
 		return fmt.Errorf("skillStore.AppendVersion: marshal: %w", err)
 	}
-	// seq = current max+1 for this skill (newest-first ordering key).
+	// seq = current max+1 for this skill (newest-first ordering key). The
+	// MAX-then-INSERT runs in ONE transaction and the (skill_id, seq) index is
+	// UNIQUE, so two concurrent appends can't both land the same seq: the loser
+	// fails loudly on commit instead of silently corrupting the ordering. The
+	// Scan error is propagated (was swallowed, leaving seq=0 on failure).
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("skillStore.AppendVersion: begin: %w", err)
+	}
+	defer tx.Rollback() //nolint:errcheck // no-op after Commit
 	var seq int64
-	_ = s.db.QueryRowContext(ctx, `SELECT COALESCE(MAX(seq),0)+1 FROM skill_versions WHERE skill_id = ?`, sv.SkillID).Scan(&seq)
-	if _, err := s.db.ExecContext(ctx,
+	if err := tx.QueryRowContext(ctx, `SELECT COALESCE(MAX(seq),0)+1 FROM skill_versions WHERE skill_id = ?`, sv.SkillID).Scan(&seq); err != nil {
+		return fmt.Errorf("skillStore.AppendVersion: seq: %w", err)
+	}
+	if _, err := tx.ExecContext(ctx,
 		`INSERT INTO skill_versions (id, skill_id, version, seq, data) VALUES (?, ?, ?, ?, ?)`,
 		sv.ID, sv.SkillID, sv.Version, seq, string(blob)); err != nil {
-		return fmt.Errorf("skillStore.AppendVersion: %w", err)
+		return fmt.Errorf("skillStore.AppendVersion: insert: %w", err)
+	}
+	if err := tx.Commit(); err != nil {
+		return fmt.Errorf("skillStore.AppendVersion: commit: %w", err)
 	}
 	return nil
 }