feat: add nixpkgs-search binary with package search support

Add a new nixpkgs-search CLI that combines NixOS options search with
Nix package search functionality. This provides two MCP servers from
a single binary:
- `nixpkgs-search options serve` for NixOS options
- `nixpkgs-search packages serve` for Nix packages

Key changes:
- Add packages table to database schema (version 3)
- Add Package type and search methods to database layer
- Create internal/packages/ with indexer and parser for nix-env JSON
- Add MCP server mode (options/packages) with separate tool sets
- Add package handlers: search_packages, get_package
- Create cmd/nixpkgs-search with combined indexing support
- Update flake.nix with nixpkgs-search package (now default)
- Bump version to 0.2.0

The index command can index both options and packages together, or
use --no-packages/--no-options flags for partial indexing.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

internal/database/sqlite.go

@@ -44,10 +44,12 @@ func (s *SQLiteStore) Initialize(ctx context.Context) error {
 		dropStmts := []string{
 			DropDeclarations,
 			DropOptions,
+			DropPackages,
 			DropFiles,
 			DropRevisions,
 			DropSchemaInfo,
 			"DROP TABLE IF EXISTS options_fts",
+			"DROP TABLE IF EXISTS packages_fts",
 		}
 		for _, stmt := range dropStmts {
 			if _, err := s.db.ExecContext(ctx, stmt); err != nil {
@@ -63,10 +65,13 @@ func (s *SQLiteStore) Initialize(ctx context.Context) error {
 		OptionsTable,
 		DeclarationsTable,
 		FilesTable,
+		PackagesTable,
 		IndexOptionsRevisionName,
 		IndexOptionsRevisionParent,
 		IndexFilesRevisionPath,
 		IndexDeclarationsOption,
+		IndexPackagesRevisionAttr,
+		IndexPackagesRevisionPname,
 	}
 
 	for _, stmt := range createStmts {
@@ -88,8 +93,8 @@ func (s *SQLiteStore) Initialize(ctx context.Context) error {
 		return fmt.Errorf("failed to create FTS table: %w", err)
 	}
 
-	// Create triggers to keep FTS in sync
-	triggers := []string{
+	// Create triggers to keep options FTS in sync
+	optionsTriggers := []string{
 		`CREATE TRIGGER IF NOT EXISTS options_ai AFTER INSERT ON options BEGIN
 			INSERT INTO options_fts(rowid, name, description) VALUES (new.id, new.name, new.description);
 		END`,
@@ -101,9 +106,42 @@ func (s *SQLiteStore) Initialize(ctx context.Context) error {
 			INSERT INTO options_fts(rowid, name, description) VALUES (new.id, new.name, new.description);
 		END`,
 	}
-	for _, trigger := range triggers {
+	for _, trigger := range optionsTriggers {
 		if _, err := s.db.ExecContext(ctx, trigger); err != nil {
-			return fmt.Errorf("failed to create trigger: %w", err)
+			return fmt.Errorf("failed to create options trigger: %w", err)
+		}
+	}
+
+	// Create FTS5 virtual table for packages full-text search
+	_, err = s.db.ExecContext(ctx, `
+		CREATE VIRTUAL TABLE IF NOT EXISTS packages_fts USING fts5(
+			attr_path,
+			pname,
+			description,
+			content='packages',
+			content_rowid='id'
+		)
+	`)
+	if err != nil {
+		return fmt.Errorf("failed to create packages FTS table: %w", err)
+	}
+
+	// Create triggers to keep packages FTS in sync
+	packagesTriggers := []string{
+		`CREATE TRIGGER IF NOT EXISTS packages_ai AFTER INSERT ON packages BEGIN
+			INSERT INTO packages_fts(rowid, attr_path, pname, description) VALUES (new.id, new.attr_path, new.pname, new.description);
+		END`,
+		`CREATE TRIGGER IF NOT EXISTS packages_ad AFTER DELETE ON packages BEGIN
+			INSERT INTO packages_fts(packages_fts, rowid, attr_path, pname, description) VALUES('delete', old.id, old.attr_path, old.pname, old.description);
+		END`,
+		`CREATE TRIGGER IF NOT EXISTS packages_au AFTER UPDATE ON packages BEGIN
+			INSERT INTO packages_fts(packages_fts, rowid, attr_path, pname, description) VALUES('delete', old.id, old.attr_path, old.pname, old.description);
+			INSERT INTO packages_fts(rowid, attr_path, pname, description) VALUES (new.id, new.attr_path, new.pname, new.description);
+		END`,
+	}
+	for _, trigger := range packagesTriggers {
+		if _, err := s.db.ExecContext(ctx, trigger); err != nil {
+			return fmt.Errorf("failed to create packages trigger: %w", err)
 		}
 	}
 
@@ -127,9 +165,9 @@ func (s *SQLiteStore) Close() error {
 // CreateRevision creates a new revision record.
 func (s *SQLiteStore) CreateRevision(ctx context.Context, rev *Revision) error {
 	result, err := s.db.ExecContext(ctx, `
-		INSERT INTO revisions (git_hash, channel_name, commit_date, option_count)
-		VALUES (?, ?, ?, ?)`,
-		rev.GitHash, rev.ChannelName, rev.CommitDate, rev.OptionCount,
+		INSERT INTO revisions (git_hash, channel_name, commit_date, option_count, package_count)
+		VALUES (?, ?, ?, ?, ?)`,
+		rev.GitHash, rev.ChannelName, rev.CommitDate, rev.OptionCount, rev.PackageCount,
 	)
 	if err != nil {
 		return fmt.Errorf("failed to create revision: %w", err)
@@ -155,9 +193,9 @@ func (s *SQLiteStore) CreateRevision(ctx context.Context, rev *Revision) error {
 func (s *SQLiteStore) GetRevision(ctx context.Context, gitHash string) (*Revision, error) {
 	rev := &Revision{}
 	err := s.db.QueryRowContext(ctx, `
-		SELECT id, git_hash, channel_name, commit_date, indexed_at, option_count
+		SELECT id, git_hash, channel_name, commit_date, indexed_at, option_count, package_count
 		FROM revisions WHERE git_hash = ?`, gitHash,
-	).Scan(&rev.ID, &rev.GitHash, &rev.ChannelName, &rev.CommitDate, &rev.IndexedAt, &rev.OptionCount)
+	).Scan(&rev.ID, &rev.GitHash, &rev.ChannelName, &rev.CommitDate, &rev.IndexedAt, &rev.OptionCount, &rev.PackageCount)
 	if err == sql.ErrNoRows {
 		return nil, nil
 	}
@@ -171,10 +209,10 @@ func (s *SQLiteStore) GetRevision(ctx context.Context, gitHash string) (*Revisio
 func (s *SQLiteStore) GetRevisionByChannel(ctx context.Context, channel string) (*Revision, error) {
 	rev := &Revision{}
 	err := s.db.QueryRowContext(ctx, `
-		SELECT id, git_hash, channel_name, commit_date, indexed_at, option_count
+		SELECT id, git_hash, channel_name, commit_date, indexed_at, option_count, package_count
 		FROM revisions WHERE channel_name = ?
 		ORDER BY indexed_at DESC LIMIT 1`, channel,
-	).Scan(&rev.ID, &rev.GitHash, &rev.ChannelName, &rev.CommitDate, &rev.IndexedAt, &rev.OptionCount)
+	).Scan(&rev.ID, &rev.GitHash, &rev.ChannelName, &rev.CommitDate, &rev.IndexedAt, &rev.OptionCount, &rev.PackageCount)
 	if err == sql.ErrNoRows {
 		return nil, nil
 	}
@@ -187,17 +225,17 @@ func (s *SQLiteStore) GetRevisionByChannel(ctx context.Context, channel string)
 // ListRevisions returns all indexed revisions.
 func (s *SQLiteStore) ListRevisions(ctx context.Context) ([]*Revision, error) {
 	rows, err := s.db.QueryContext(ctx, `
-		SELECT id, git_hash, channel_name, commit_date, indexed_at, option_count
+		SELECT id, git_hash, channel_name, commit_date, indexed_at, option_count, package_count
 		FROM revisions ORDER BY indexed_at DESC`)
 	if err != nil {
 		return nil, fmt.Errorf("failed to list revisions: %w", err)
 	}
-	defer rows.Close() //nolint:errcheck // rows.Err() checked after iteration //nolint:errcheck // rows.Err() checked after iteration
+	defer rows.Close() //nolint:errcheck // rows.Err() checked after iteration
 
 	var revisions []*Revision
 	for rows.Next() {
 		rev := &Revision{}
-		if err := rows.Scan(&rev.ID, &rev.GitHash, &rev.ChannelName, &rev.CommitDate, &rev.IndexedAt, &rev.OptionCount); err != nil {
+		if err := rows.Scan(&rev.ID, &rev.GitHash, &rev.ChannelName, &rev.CommitDate, &rev.IndexedAt, &rev.OptionCount, &rev.PackageCount); err != nil {
 			return nil, fmt.Errorf("failed to scan revision: %w", err)
 		}
 		revisions = append(revisions, rev)
@@ -588,6 +626,138 @@ func (s *SQLiteStore) GetFileWithRange(ctx context.Context, revisionID int64, pa
 	return applyLineRange(file, r), nil
 }
 
+// CreatePackage creates a new package record.
+func (s *SQLiteStore) CreatePackage(ctx context.Context, pkg *Package) error {
+	result, err := s.db.ExecContext(ctx, `
+		INSERT INTO packages (revision_id, attr_path, pname, version, description, long_description, homepage, license, platforms, maintainers, broken, unfree, insecure)
+		VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,
+		pkg.RevisionID, pkg.AttrPath, pkg.Pname, pkg.Version, pkg.Description, pkg.LongDescription, pkg.Homepage, pkg.License, pkg.Platforms, pkg.Maintainers, pkg.Broken, pkg.Unfree, pkg.Insecure,
+	)
+	if err != nil {
+		return fmt.Errorf("failed to create package: %w", err)
+	}
+
+	id, err := result.LastInsertId()
+	if err != nil {
+		return fmt.Errorf("failed to get last insert id: %w", err)
+	}
+	pkg.ID = id
+	return nil
+}
+
+// CreatePackagesBatch creates multiple packages in a batch.
+func (s *SQLiteStore) CreatePackagesBatch(ctx context.Context, pkgs []*Package) error {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer tx.Rollback() //nolint:errcheck // rollback after commit returns error, which is expected
+
+	stmt, err := tx.PrepareContext(ctx, `
+		INSERT INTO packages (revision_id, attr_path, pname, version, description, long_description, homepage, license, platforms, maintainers, broken, unfree, insecure)
+		VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`)
+	if err != nil {
+		return fmt.Errorf("failed to prepare statement: %w", err)
+	}
+	defer stmt.Close() //nolint:errcheck // statement closed with transaction
+
+	for _, pkg := range pkgs {
+		result, err := stmt.ExecContext(ctx,
+			pkg.RevisionID, pkg.AttrPath, pkg.Pname, pkg.Version, pkg.Description, pkg.LongDescription, pkg.Homepage, pkg.License, pkg.Platforms, pkg.Maintainers, pkg.Broken, pkg.Unfree, pkg.Insecure,
+		)
+		if err != nil {
+			return fmt.Errorf("failed to insert package %s: %w", pkg.AttrPath, err)
+		}
+		id, err := result.LastInsertId()
+		if err != nil {
+			return fmt.Errorf("failed to get last insert id: %w", err)
+		}
+		pkg.ID = id
+	}
+
+	return tx.Commit()
+}
+
+// GetPackage retrieves a package by revision and attr_path.
+func (s *SQLiteStore) GetPackage(ctx context.Context, revisionID int64, attrPath string) (*Package, error) {
+	pkg := &Package{}
+	err := s.db.QueryRowContext(ctx, `
+		SELECT id, revision_id, attr_path, pname, version, description, long_description, homepage, license, platforms, maintainers, broken, unfree, insecure
+		FROM packages WHERE revision_id = ? AND attr_path = ?`, revisionID, attrPath,
+	).Scan(&pkg.ID, &pkg.RevisionID, &pkg.AttrPath, &pkg.Pname, &pkg.Version, &pkg.Description, &pkg.LongDescription, &pkg.Homepage, &pkg.License, &pkg.Platforms, &pkg.Maintainers, &pkg.Broken, &pkg.Unfree, &pkg.Insecure)
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("failed to get package: %w", err)
+	}
+	return pkg, nil
+}
+
+// SearchPackages searches for packages matching a query.
+func (s *SQLiteStore) SearchPackages(ctx context.Context, revisionID int64, query string, filters PackageSearchFilters) ([]*Package, error) {
+	baseQuery := `
+		SELECT p.id, p.revision_id, p.attr_path, p.pname, p.version, p.description, p.long_description, p.homepage, p.license, p.platforms, p.maintainers, p.broken, p.unfree, p.insecure
+		FROM packages p
+		INNER JOIN packages_fts fts ON p.id = fts.rowid
+		WHERE p.revision_id = ?
+		AND packages_fts MATCH ?`
+
+	// Escape the query for FTS5 by wrapping in double quotes for literal matching.
+	escapedQuery := `"` + strings.ReplaceAll(query, `"`, `""`) + `"`
+	args := []interface{}{revisionID, escapedQuery}
+
+	if filters.Broken != nil {
+		baseQuery += " AND p.broken = ?"
+		args = append(args, *filters.Broken)
+	}
+
+	if filters.Unfree != nil {
+		baseQuery += " AND p.unfree = ?"
+		args = append(args, *filters.Unfree)
+	}
+
+	if filters.Insecure != nil {
+		baseQuery += " AND p.insecure = ?"
+		args = append(args, *filters.Insecure)
+	}
+
+	baseQuery += " ORDER BY p.attr_path"
+
+	if filters.Limit > 0 {
+		baseQuery += fmt.Sprintf(" LIMIT %d", filters.Limit)
+	}
+	if filters.Offset > 0 {
+		baseQuery += fmt.Sprintf(" OFFSET %d", filters.Offset)
+	}
+
+	rows, err := s.db.QueryContext(ctx, baseQuery, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to search packages: %w", err)
+	}
+	defer rows.Close() //nolint:errcheck // rows.Err() checked after iteration
+
+	var packages []*Package
+	for rows.Next() {
+		pkg := &Package{}
+		if err := rows.Scan(&pkg.ID, &pkg.RevisionID, &pkg.AttrPath, &pkg.Pname, &pkg.Version, &pkg.Description, &pkg.LongDescription, &pkg.Homepage, &pkg.License, &pkg.Platforms, &pkg.Maintainers, &pkg.Broken, &pkg.Unfree, &pkg.Insecure); err != nil {
+			return nil, fmt.Errorf("failed to scan package: %w", err)
+		}
+		packages = append(packages, pkg)
+	}
+	return packages, rows.Err()
+}
+
+// UpdateRevisionPackageCount updates the package count for a revision.
+func (s *SQLiteStore) UpdateRevisionPackageCount(ctx context.Context, id int64, count int) error {
+	_, err := s.db.ExecContext(ctx,
+		"UPDATE revisions SET package_count = ? WHERE id = ?", count, id)
+	if err != nil {
+		return fmt.Errorf("failed to update package count: %w", err)
+	}
+	return nil
+}
+
 // countLines counts the number of lines in content.
 func countLines(content string) int {
 	if content == "" {