Move schema_migrations table creation into 000.sql with INTEGER version column

Replace the monolithic schema.sql embed with a numbered migration system
following the pixa pattern:

- Add schema/000.sql: bootstrap migration creating schema_migrations table
  with INTEGER PRIMARY KEY version column and applied_at timestamp
- Move full schema to schema/001.sql (renamed from schema.sql)
- Remove redundant schema/008_uploads.sql (uploads table already in main schema)
- Rewrite database.go migration logic:
  - Embed schema/*.sql directory instead of single schema.sql
  - bootstrapMigrationsTable() checks for table existence, applies 000.sql
  - applyMigrations() iterates numbered files, skips already-applied versions
  - ParseMigrationVersion() extracts version from filenames (e.g. 001.sql)
  - Go code does zero INSERTs for bootstrap — 000.sql is self-contained
- Update database_test.go to verify schema_migrations table exists

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
+// Schema is managed via numbered SQL migrations embedded in the schema/
-// the local database and perform a full backup to recreate it.
+// 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
+//go:embed schema/*.sql
-var schemaSQL string
+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 {
+// collectMigrations reads the embedded schema directory and returns
-	_, err := db.conn.ExecContext(ctx, schemaSQL)
+// migration filenames sorted lexicographically.
-	return err
+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.

internal/database/database_test.go

@@ -26,9 +26,10 @@ func TestDatabase(t *testing.T) {
 		t.Fatal("database connection is nil")
 	}
 
-	// Test schema creation (already done in New)
+	// Test schema creation (already done in New via migrations)
 	// Verify tables exist
 	tables := []string{
+		"schema_migrations",
 		"files", "file_chunks", "chunks", "blobs",
 		"blob_chunks", "chunk_files", "snapshots",
 	}

internal/database/schema/000.sql

@@ -0,0 +1,9 @@
+-- Migration 000: Schema migrations tracking table
+-- Applied as a bootstrap step before the normal migration loop.
+
+CREATE TABLE IF NOT EXISTS schema_migrations (
+    version INTEGER PRIMARY KEY,
+    applied_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+INSERT OR IGNORE INTO schema_migrations (version) VALUES (0);

internal/database/schema/001.sql

@@ -1,6 +1,5 @@
--- Vaultik Database Schema
+-- Migration 001: Initial Vaultik schema
--- Note: This database does not support migrations. If the schema changes,
+-- All core tables for tracking files, chunks, blobs, snapshots, and uploads.
--- delete the local database and perform a full backup to recreate it.
 
 -- Files table: stores metadata about files in the filesystem
 CREATE TABLE IF NOT EXISTS files (
@@ -133,4 +132,4 @@ CREATE TABLE IF NOT EXISTS uploads (
 );
 
 -- Index for efficient snapshot lookups
-CREATE INDEX IF NOT EXISTS idx_uploads_snapshot_id ON uploads(snapshot_id);
+CREATE INDEX IF NOT EXISTS idx_uploads_snapshot_id ON uploads(snapshot_id);

internal/database/schema/008_uploads.sql

@@ -1,11 +0,0 @@
--- Track blob upload metrics
-CREATE TABLE IF NOT EXISTS uploads (
-    blob_hash TEXT PRIMARY KEY,
-    uploaded_at TIMESTAMP NOT NULL,
-    size INTEGER NOT NULL,
-    duration_ms INTEGER NOT NULL,
-    FOREIGN KEY (blob_hash) REFERENCES blobs(blob_hash)
-);
-
-CREATE INDEX idx_uploads_uploaded_at ON uploads(uploaded_at);
-CREATE INDEX idx_uploads_duration ON uploads(duration_ms);