Move schema_migrations table creation into 000.sql with INTEGER version column (#58)

Closes #57

Adopts the [pixa migration pattern](sneak/pixa#36) for schema management. Replaces the monolithic `schema.sql` embed with a numbered migration system.

## Changes

### New: `schema/000.sql` — Bootstrap migration
- Creates `schema_migrations` table with `INTEGER PRIMARY KEY` version column
- Self-contained: includes both `CREATE TABLE IF NOT EXISTS` and `INSERT OR IGNORE` for version 0
- Go code does zero INSERTs for bootstrap — just reads and executes 000.sql

### Renamed: `schema.sql` → `schema/001.sql` — Initial schema migration
- Full Vaultik schema (files, chunks, blobs, snapshots, uploads, all indexes)
- Updated header comment to identify it as migration 001

### Removed: `schema/008_uploads.sql`
- Redundant — the uploads table with its current schema was already in the main schema file
- The 008 file had a stale/different schema (TIMESTAMP instead of INTEGER, missing snapshot_id FK)

### Rewritten: `database.go` — Migration engine
- `//go:embed schema/*.sql` replaces `//go:embed schema.sql`
- `bootstrapMigrationsTable()`: checks if `schema_migrations` table exists, applies 000.sql if missing
- `applyMigrations()`: iterates through numbered .sql files, checks `schema_migrations` for each version, applies and records pending ones
- `collectMigrations()`: reads embedded schema dir, returns sorted filenames
- `ParseMigrationVersion()`: extracts numeric version from filenames like `001.sql` or `001_description.sql` (exported for testing)
- Old `createSchema()` removed entirely

### Updated: `database_test.go`
- Verifies `schema_migrations` table exists alongside other core tables

## Verification

`docker build .` passes — formatting, linting, all tests green.

Co-authored-by: clawbot <clawbot@noreply.git.eeqj.de>
Reviewed-on: #58
Co-authored-by: clawbot <clawbot@noreply.example.org>
Co-committed-by: clawbot <clawbot@noreply.example.org>

internal/database/database.go

@@ -6,24 +6,32 @@
 // multiple source files. Blobs are content-addressed, meaning their filename
 // is derived from their SHA256 hash after compression and encryption.
 //
-// The database does not support migrations. If the schema changes, delete
-// the local database and perform a full backup to recreate it.
+// Schema is managed via numbered SQL migrations embedded in the schema/
+// directory. Migration 000.sql bootstraps the schema_migrations tracking
+// table; subsequent migrations (001, 002, …) are applied in order.
 package database
 
 import (
 	"context"
 	"database/sql"
-	_ "embed"
+	"embed"
 	"fmt"
 	"os"
+	"path/filepath"
+	"sort"
+	"strconv"
 	"strings"
 
 	"git.eeqj.de/sneak/vaultik/internal/log"
 	_ "modernc.org/sqlite"
 )
 
-//go:embed schema.sql
-var schemaSQL string
+//go:embed schema/*.sql
+var schemaFS embed.FS
+
+// bootstrapVersion is the migration that creates the schema_migrations
+// table itself. It is applied before the normal migration loop.
+const bootstrapVersion = 0
 
 // DB represents the Vaultik local index database connection.
 // It uses SQLite to track file metadata, content-defined chunks, and blob associations.
@@ -35,6 +43,46 @@ type DB struct {
 	path string
 }
 
+// ParseMigrationVersion extracts the numeric version prefix from a migration
+// filename. Filenames must follow the pattern "<version>.sql" or
+// "<version>_<description>.sql", where version is a zero-padded numeric
+// string (e.g. "001", "002"). Returns the version as an integer and an
+// error if the filename does not match the expected pattern.
+func ParseMigrationVersion(filename string) (int, error) {
+	name := strings.TrimSuffix(filename, filepath.Ext(filename))
+	if name == "" {
+		return 0, fmt.Errorf("invalid migration filename %q: empty name", filename)
+	}
+
+	// Split on underscore to separate version from description.
+	// If there's no underscore, the entire stem is the version.
+	versionStr := name
+	if idx := strings.IndexByte(name, '_'); idx >= 0 {
+		versionStr = name[:idx]
+	}
+
+	if versionStr == "" {
+		return 0, fmt.Errorf("invalid migration filename %q: empty version prefix", filename)
+	}
+
+	// Validate the version is purely numeric.
+	for _, ch := range versionStr {
+		if ch < '0' || ch > '9' {
+			return 0, fmt.Errorf(
+				"invalid migration filename %q: version %q contains non-numeric character %q",
+				filename, versionStr, string(ch),
+			)
+		}
+	}
+
+	version, err := strconv.Atoi(versionStr)
+	if err != nil {
+		return 0, fmt.Errorf("invalid migration filename %q: %w", filename, err)
+	}
+
+	return version, nil
+}
+
 // New creates a new database connection at the specified path.
 // It creates the schema if needed and configures SQLite with WAL mode for
 // better concurrency. SQLite handles crash recovery automatically when
@@ -72,9 +120,9 @@ func New(ctx context.Context, path string) (*DB, error) {
 			}
 
 			db := &DB{conn: conn, path: path}
-			if err := db.createSchema(ctx); err != nil {
+			if err := applyMigrations(ctx, conn); err != nil {
 				_ = conn.Close()
-				return nil, fmt.Errorf("creating schema: %w", err)
+				return nil, fmt.Errorf("applying migrations: %w", err)
 			}
 			return db, nil
 		}
@@ -125,9 +173,9 @@ func New(ctx context.Context, path string) (*DB, error) {
 	}
 
 	db := &DB{conn: conn, path: path}
-	if err := db.createSchema(ctx); err != nil {
+	if err := applyMigrations(ctx, conn); err != nil {
 		_ = conn.Close()
-		return nil, fmt.Errorf("creating schema: %w", err)
+		return nil, fmt.Errorf("applying migrations: %w", err)
 	}
 
 	log.Debug("Database connection established successfully", "path", path)
@@ -198,9 +246,120 @@ func (db *DB) QueryRowWithLog(
 	return db.conn.QueryRowContext(ctx, query, args...)
 }
 
-func (db *DB) createSchema(ctx context.Context) error {
-	_, err := db.conn.ExecContext(ctx, schemaSQL)
-	return err
+// collectMigrations reads the embedded schema directory and returns
+// migration filenames sorted lexicographically.
+func collectMigrations() ([]string, error) {
+	entries, err := schemaFS.ReadDir("schema")
+	if err != nil {
+		return nil, fmt.Errorf("failed to read schema directory: %w", err)
+	}
+
+	var migrations []string
+
+	for _, entry := range entries {
+		if !entry.IsDir() && strings.HasSuffix(entry.Name(), ".sql") {
+			migrations = append(migrations, entry.Name())
+		}
+	}
+
+	sort.Strings(migrations)
+
+	return migrations, nil
+}
+
+// bootstrapMigrationsTable ensures the schema_migrations table exists
+// by applying 000.sql if the table is missing.
+func bootstrapMigrationsTable(ctx context.Context, db *sql.DB) error {
+	var tableExists int
+
+	err := db.QueryRowContext(ctx,
+		"SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='schema_migrations'",
+	).Scan(&tableExists)
+	if err != nil {
+		return fmt.Errorf("failed to check for migrations table: %w", err)
+	}
+
+	if tableExists > 0 {
+		return nil
+	}
+
+	content, err := schemaFS.ReadFile("schema/000.sql")
+	if err != nil {
+		return fmt.Errorf("failed to read bootstrap migration 000.sql: %w", err)
+	}
+
+	log.Info("applying bootstrap migration", "version", bootstrapVersion)
+
+	_, err = db.ExecContext(ctx, string(content))
+	if err != nil {
+		return fmt.Errorf("failed to apply bootstrap migration: %w", err)
+	}
+
+	return nil
+}
+
+// applyMigrations applies all pending migrations to db. It first bootstraps
+// the schema_migrations table via 000.sql, then iterates through remaining
+// migration files in order.
+func applyMigrations(ctx context.Context, db *sql.DB) error {
+	if err := bootstrapMigrationsTable(ctx, db); err != nil {
+		return err
+	}
+
+	migrations, err := collectMigrations()
+	if err != nil {
+		return err
+	}
+
+	for _, migration := range migrations {
+		version, parseErr := ParseMigrationVersion(migration)
+		if parseErr != nil {
+			return parseErr
+		}
+
+		// Check if already applied.
+		var count int
+
+		err := db.QueryRowContext(ctx,
+			"SELECT COUNT(*) FROM schema_migrations WHERE version = ?",
+			version,
+		).Scan(&count)
+		if err != nil {
+			return fmt.Errorf("failed to check migration status: %w", err)
+		}
+
+		if count > 0 {
+			log.Debug("migration already applied", "version", version)
+
+			continue
+		}
+
+		// Read and apply migration.
+		content, readErr := schemaFS.ReadFile(filepath.Join("schema", migration))
+		if readErr != nil {
+			return fmt.Errorf("failed to read migration %s: %w", migration, readErr)
+		}
+
+		log.Info("applying migration", "version", version)
+
+		_, execErr := db.ExecContext(ctx, string(content))
+		if execErr != nil {
+			return fmt.Errorf("failed to apply migration %s: %w", migration, execErr)
+		}
+
+		// Record migration as applied.
+		_, recErr := db.ExecContext(ctx,
+			"INSERT INTO schema_migrations (version) VALUES (?)",
+			version,
+		)
+		if recErr != nil {
+			return fmt.Errorf("failed to record migration %s: %w", migration, recErr)
+		}
+
+		log.Info("migration applied successfully", "version", version)
+	}
+
+	return nil
 }
 
 // NewTestDB creates an in-memory SQLite database for testing purposes.