feat(types): add template molecules infrastructure for beads-1ra

Add support for template molecules (is_template field and TypeMolecule type):

- Add IsTemplate field to Issue type with JSON support
- Add TypeMolecule constant to IssueType constants
- Add IsTemplate filter to IssueFilter for querying
- Update all SQL queries to include is_template column
- Add migration 024 for is_template column
- Add FindMoleculesJSONLInDir helper for molecules.jsonl path detection

This enables treating certain issues as read-only templates that can be
instantiated to create work items. The template flag allows separating
template molecules from regular work items in queries and exports.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

internal/storage/sqlite/migrations/024_is_template_column.go

@@ -0,0 +1,40 @@
+package migrations
+
+import (
+	"database/sql"
+	"fmt"
+)
+
+// MigrateIsTemplateColumn adds the is_template column to the issues table.
+// Template issues (molecules) are read-only templates that should be filtered
+// from work views by default (beads-1ra).
+func MigrateIsTemplateColumn(db *sql.DB) error {
+	// Check if column already exists
+	var columnExists bool
+	err := db.QueryRow(`
+		SELECT COUNT(*) > 0
+		FROM pragma_table_info('issues')
+		WHERE name = 'is_template'
+	`).Scan(&columnExists)
+	if err != nil {
+		return fmt.Errorf("failed to check is_template column: %w", err)
+	}
+
+	if columnExists {
+		return nil
+	}
+
+	// Add the is_template column
+	_, err = db.Exec(`ALTER TABLE issues ADD COLUMN is_template INTEGER DEFAULT 0`)
+	if err != nil {
+		return fmt.Errorf("failed to add is_template column: %w", err)
+	}
+
+	// Add index for template issues (for efficient filtering)
+	_, err = db.Exec(`CREATE INDEX IF NOT EXISTS idx_issues_is_template ON issues(is_template) WHERE is_template = 1`)
+	if err != nil {
+		return fmt.Errorf("failed to create is_template index: %w", err)
+	}
+
+	return nil
+}