Restructure system prompt with softer tone

[akseljoonas]

Summary

• Adopts the research loop structure, SOTA check, scope discipline, and consolidated sections from the imperative prompt rewrite
• Restores the original advisory tone — removes "MUST", "No exceptions", "These are not hypothetical" language
• Same content and rules, presented as guidance rather than commands

Test plan

• Review diff to confirm no content/rules were lost
• Run agent on a sample task to verify prompt behavior is unchanged