themida: sync docs with current passing sample

[NaC-L]

Summary

• update Themida-facing docs and manifest commentary to match the current passing example2-virt.bin behavior
• keep autoresearch.sh in the simpler tee-based form after the PowerShell-only rewrite showed no benchmark or capture benefit

Verification

• python test.py themida
• bash autoresearch.sh

Notes

• run_experiment still records an empty benchmark.log with null parsed metrics on this workstation across direct, cmd, bash, and PowerShell launch shapes
• this branch does not change lifter behavior; it syncs docs and notes with the current green Themida gate