refactor: extract prepare_query helper for exec/trace commands

[zharinov]

Summary

• Extract duplicated query setup logic from exec.rs and trace.rs into run_common::prepare_query()
• Add QueryInput struct for common parameters and PreparedQuery struct for results
• Reduce exec.rs by 45 lines, trace.rs by 45 lines

Why

Both exec and trace commands had ~55 identical lines for: validate inputs → load query → parse → analyze → link → check diagnostics → emit bytecode → load module → resolve entrypoint → parse tree → build trivia. Consolidating this makes future changes easier and reduces bug surface area.