feat: sqlite persistence with goose migrations, flashcard schema, zap logger

- Add SQLite as authoritative store alongside Qdrant (best-effort indexing)
- Use goose for embedded SQL migrations
- Schema matches flashcard format: id(INTEGER PK), note, repos, host, tags, user, context, created
- Replace std log with zap structured logger
- Split registerTools into registerStoreKnowledge + registerSearchKnowledge
- Qdrant index uses SQLite rowid directly as point ID (no SHA256 hash)
- Search enriches Qdrant results from SQLite by ID
- Lowercase auth header before prefix check
- Always handle json.MarshalIndent errors
- NixOS: StateDirectory, sqlitePath to /var/lib/st-pierre/st-pierre.sqlite

sqlite.go

@@ -0,0 +1,148 @@
+package main
+
+import (
+	"context"
+	"database/sql"
+	"embed"
+	"encoding/json"
+	"fmt"
+	"strings"
+
+	"github.com/pressly/goose/v3"
+	_ "modernc.org/sqlite"
+)
+
+//go:embed migrations/*.sql
+var embedMigrations embed.FS
+
+type sqliteStore struct {
+	db *sql.DB
+}
+
+func newSqliteStore(path string) (*sqliteStore, error) {
+	db, err := sql.Open("sqlite", path)
+	if err != nil {
+		return nil, fmt.Errorf("open sqlite: %w", err)
+	}
+
+	db.SetMaxOpenConns(1)
+
+	goose.SetBaseFS(embedMigrations)
+
+	if err := goose.SetDialect("sqlite3"); err != nil {
+		db.Close()
+		return nil, fmt.Errorf("set dialect: %w", err)
+	}
+
+	if err := goose.Up(db, "migrations"); err != nil {
+		db.Close()
+		return nil, fmt.Errorf("migrate: %w", err)
+	}
+
+	return &sqliteStore{db: db}, nil
+}
+
+func (s *sqliteStore) save(ctx context.Context, note, host, user, context_ string, repos, tags []string) (int64, error) {
+	reposJSON := marshalStringSlice(repos)
+	tagsJSON := marshalStringSlice(tags)
+
+	result, err := s.db.ExecContext(ctx,
+		`INSERT INTO knowledge (note, repos, host, tags, "user", context)
+		 VALUES (?, ?, ?, ?, ?, ?)`,
+		note, reposJSON, host, tagsJSON, user, context_,
+	)
+	if err != nil {
+		return 0, fmt.Errorf("insert: %w", err)
+	}
+
+	id, err := result.LastInsertId()
+	if err != nil {
+		return 0, fmt.Errorf("last insert id: %w", err)
+	}
+
+	return id, nil
+}
+
+func (s *sqliteStore) getByID(ctx context.Context, id int64) (*entry, error) {
+	row := s.db.QueryRowContext(ctx,
+		`SELECT id, note, repos, host, tags, "user", context, created
+		 FROM knowledge WHERE id = ?`, id,
+	)
+
+	var e entry
+	var reposJSON, tagsJSON sql.NullString
+	var host, user, context_ sql.NullString
+
+	err := row.Scan(&e.ID, &e.Note, &reposJSON, &host, &tagsJSON, &user, &context_, &e.Created)
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("query: %w", err)
+	}
+
+	if reposJSON.Valid {
+		e.Repos = unmarshalStringSlice(reposJSON.String)
+	}
+	if tagsJSON.Valid {
+		e.Tags = unmarshalStringSlice(tagsJSON.String)
+	}
+	if host.Valid {
+		e.Host = host.String
+	}
+	if user.Valid {
+		e.User = user.String
+	}
+	if context_.Valid {
+		e.Context = context_.String
+	}
+
+	return &e, nil
+}
+
+func (s *sqliteStore) close() error {
+	return s.db.Close()
+}
+
+func marshalStringSlice(ss []string) string {
+	if len(ss) == 0 {
+		return "[]"
+	}
+	b, _ := json.Marshal(ss)
+	return string(b)
+}
+
+func unmarshalStringSlice(raw string) []string {
+	if raw == "" || raw == "[]" || raw == "null" {
+		return nil
+	}
+	var ss []string
+	if err := json.Unmarshal([]byte(raw), &ss); err != nil {
+		return nil
+	}
+	return ss
+}
+
+func parseStringSlice(raw any) []string {
+	if raw == nil {
+		return nil
+	}
+	arr, ok := raw.([]any)
+	if !ok {
+		return nil
+	}
+	result := make([]string, 0, len(arr))
+	for _, v := range arr {
+		if s, ok := v.(string); ok {
+			result = append(result, s)
+		}
+	}
+	return result
+}
+
+func parseOptionalString(raw any) string {
+	if s, ok := raw.(string); ok && strings.TrimSpace(s) != "" {
+		return s
+	}
+	return ""
+}