Break the hardcoded per-sub-q filter prompt into 3 editable PromptService templates (filter_intro, filter_section, filter_outro) with placeholders for the for-loop iteration pattern. Refactor RelevanceFilter._build_per_subq_prompt() to compose them at runtime, falling back to built-in defaults when PromptService is unavailable.
Fix two latent bugs from Package 4:
- generate_per_subq was called by rag.py but never added to _VALID_STEPS or DB seed (would ValueError at runtime)
- _SEED_GENERATE placeholder mismatch: flat generate_response() expects {question}/{context} but Package 4 changed it to {context_sections}. Restored flat template; generate_per_subq now holds {context_sections}.
Add database backfill migration in seed_default_profiles() to INSERT OR IGNORE missing steps into existing profile rows, ensuring all 7 steps exist on restart.
Restructure System Prompts UI: remove unused flat filter/generate steps, replace with Step 2.1-2.3 (filter_intro/section/outro) and Step 3 (generate_per_subq). Update PlaceholderDocs with {context_sections}, {subq_idx}, {subq_question}.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add chunks_retrieved_per_subq_count and chunks_filtered_per_subq_count columns to query_history table with safe ALTER TABLE migration. Replace generate template {question}/{context} placeholders with {context_sections} for per-sub-question organized context sections. Update Phase 3 test assertions to match new template and schema shapes.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Woody