feat(db): update history schema and generate prompt template for Package 4

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>

backend/app/core/sqlite_db.py

@@ -22,13 +22,14 @@ _SEED_FILTER = (
 )
 
 _SEED_GENERATE = (
-    "Question: {question}\n\n"
-    "Answer the question using ONLY these document chunks. "
-    "Do not use any external knowledge. "
-    "Format your answer as bullet points. "
-    "Cite your sources inline using the exact bracket labels provided, "
-    "e.g. [filename, page N]. Place the citation at the end of each relevant point.\n\n"
-    "Document chunks:\n{context}\n\n"
+    "You must answer each sub-question using ONLY the document chunks provided for it.\n"
+    "Do not use any external knowledge.\n"
+    "Format your answer as markdown sections — one section per sub-question.\n"
+    "Each section should start with \"## Sub-question N: <the question>\"\n"
+    "Each section should contain 1-5 bullet points.\n"
+    "Cite your sources inline using bracket labels, e.g. [filename, page N].\n"
+    "Place the citation at the end of each relevant bullet point.\n\n"
+    "{context_sections}\n\n"
     "Answer:"
 )
 
@@ -113,6 +114,8 @@ def init_history_db(conn: sqlite3.Connection) -> None:
             final_answer TEXT DEFAULT NULL,
             sources TEXT DEFAULT NULL,
             profile_used TEXT DEFAULT NULL,
+            chunks_retrieved_per_subq_count TEXT DEFAULT NULL,
+            chunks_filtered_per_subq_count TEXT DEFAULT NULL,
             created_at TEXT NOT NULL DEFAULT (datetime('now'))
         )
     """)
@@ -120,6 +123,13 @@ def init_history_db(conn: sqlite3.Connection) -> None:
         CREATE INDEX IF NOT EXISTS idx_query_history_created_at
         ON query_history(created_at DESC)
     """)
+    for col_name in ["chunks_retrieved_per_subq_count", "chunks_filtered_per_subq_count"]:
+        try:
+            conn.execute(
+                f"ALTER TABLE query_history ADD COLUMN {col_name} TEXT DEFAULT NULL"
+            )
+        except Exception:
+            pass
     conn.commit()
     logger.info("History DB tables initialized.")
 

backend/app/services/history_service.py

@@ -26,6 +26,7 @@ _INSERT_COLUMNS = (
     "generate_prompt", "generator_time_ms",
     "total_time_ms",
     "final_answer", "sources", "profile_used",
+    "chunks_retrieved_per_subq_count", "chunks_filtered_per_subq_count",
 )
 
 

backend/app/test/test_phase3_history_service.py

@@ -47,6 +47,8 @@ CREATE TABLE IF NOT EXISTS query_history (
     final_answer TEXT DEFAULT NULL,
     sources TEXT DEFAULT NULL,
     profile_used TEXT DEFAULT NULL,
+    chunks_retrieved_per_subq_count TEXT DEFAULT NULL,
+    chunks_filtered_per_subq_count TEXT DEFAULT NULL,
     created_at TEXT NOT NULL DEFAULT (datetime('now'))
 )
 """

backend/app/test/test_phase3_prompt_service.py

@@ -98,7 +98,7 @@ def test_get_profile_prompts_returns_all_three_steps(tmp_path):
     assert set(prompts.keys()) == {"decompose", "filter", "generate"}
     assert "{question}" in prompts["decompose"]
     assert "{question}" in prompts["filter"]
-    assert "{question}" in prompts["generate"]
+    assert "{context_sections}" in prompts["generate"]
 
 
 def test_get_profile_prompts_invalid_name_raises(tmp_path):

backend/app/test/test_phase3_sqlite_db.py

@@ -311,7 +311,7 @@ def test_seed_default_profiles_contains_expected_templates(tmp_path, monkeypatch
     assert "{question}" in filter_row["prompt_template"]
     assert "{chunks}" in filter_row["prompt_template"]
 
-    # Generate must have {question} and {context}
+    # Generate must have {context_sections}
     generate_row = conn.execute(
         """SELECT sp.prompt_template
            FROM system_prompts sp
@@ -319,8 +319,7 @@ def test_seed_default_profiles_contains_expected_templates(tmp_path, monkeypatch
            WHERE spp.name='A' AND sp.step_name='generate'"""
     ).fetchone()
     assert generate_row is not None
-    assert "{question}" in generate_row["prompt_template"]
-    assert "{context}" in generate_row["prompt_template"]
+    assert "{context_sections}" in generate_row["prompt_template"]
 
     conn.close()