test: add memory database tests and update conftest for DB isolation

conftest patches mdb._DB_PATH and calls init_db() after directory creation
so all existing tests continue to work with the new DB layer. New
test_memory_db.py covers upsert, search, remove, migration, and the
updated list_memories/lookup_memories integration paths.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/conftest.py

@@ -28,6 +28,7 @@ def tmp_pyra_home(tmp_path, monkeypatch):
 
     import pyra.plugins.loader as pl
     import pyra.plugins.executor as pe
+    import pyra.memory.database as mdb
 
     b.VAULT_PATH = fake_home / "vault"
     b.BLOCKED_PREFIXES = [b.VAULT_PATH]
@@ -35,6 +36,8 @@ def tmp_pyra_home(tmp_path, monkeypatch):
     mi._INDEX_FILE = fake_home / "memory" / "MEMORY_INDEX.md"
     mr._MEMORY_ROOT = fake_home / "memory"
     mw._MEMORY_ROOT = fake_home / "memory"
+    mdb._DB_PATH = fake_home / "memory" / "memory.db"
+    mdb._MEMORY_ROOT = fake_home / "memory"
     vr._KEYS_FILE = fake_home / "vault" / "secrets" / "api_keys.json"
     vw._KEYS_FILE = fake_home / "vault" / "secrets" / "api_keys.json"
     si._LOG_FILE = fake_home / "security.log"
@@ -52,6 +55,8 @@ def tmp_pyra_home(tmp_path, monkeypatch):
     (fake_home / "plugins").mkdir()
     (fake_home / "logs").mkdir()
 
+    mdb.init_db()
+
     # Reset plugin registry singleton so tests don't share state
     from pyra.plugins.registry import PluginRegistry
     PluginRegistry.reset()

tests/unit/test_memory_db.py

@@ -0,0 +1,119 @@
+import json
+
+
+def test_init_creates_db(tmp_pyra_home):
+    from pyra.memory import database
+    assert database._DB_PATH.exists()
+
+
+def test_upsert_and_list(tmp_pyra_home):
+    from pyra.memory import database
+    database.upsert(
+        "user/profile.md",
+        content="# Profile\n\nI am a developer.",
+        category="user",
+        size_bytes=30,
+        modified="2026-05-18T10:00:00",
+        summary="Developer profile",
+        keywords=["developer", "profile"],
+    )
+    rows = database.list_all()
+    assert len(rows) == 1
+    row = rows[0]
+    assert row["path"] == "user/profile.md"
+    assert row["category"] == "user"
+    assert row["summary"] == "Developer profile"
+    assert row["keywords"] == ["developer", "profile"]
+
+
+def test_upsert_overwrites(tmp_pyra_home):
+    from pyra.memory import database
+    database.upsert("context/notes.md", content="old", category="context",
+                    modified="2026-05-18T10:00:00")
+    database.upsert("context/notes.md", content="new", category="context",
+                    summary="updated", modified="2026-05-18T11:00:00")
+    rows = database.list_all()
+    assert len(rows) == 1
+    assert rows[0]["summary"] == "updated"
+
+
+def test_remove(tmp_pyra_home):
+    from pyra.memory import database
+    database.upsert("knowledge/facts.md", content="Some facts.", category="knowledge",
+                    modified="2026-05-18T10:00:00")
+    assert len(database.list_all()) == 1
+    database.remove("knowledge/facts.md")
+    assert len(database.list_all()) == 0
+
+
+def test_search_fts(tmp_pyra_home):
+    from pyra.memory import database
+    database.upsert("user/profile.md", content="I enjoy building AI tools.",
+                    category="user", modified="2026-05-18T10:00:00",
+                    summary="Personal bio", keywords=["AI", "tools"])
+    database.upsert("knowledge/cooking.md", content="Pasta recipes and techniques.",
+                    category="knowledge", modified="2026-05-18T10:00:00",
+                    summary="Cooking notes", keywords=["pasta", "cooking"])
+    results = database.search("AI tools")
+    assert len(results) == 1
+    assert results[0]["file"] == "user/profile.md"
+    assert results[0]["summary"] == "Personal bio"
+    assert "AI" in results[0]["keywords"]
+
+
+def test_search_no_match(tmp_pyra_home):
+    from pyra.memory import database
+    database.upsert("user/profile.md", content="Hello world.", category="user",
+                    modified="2026-05-18T10:00:00")
+    results = database.search("xyzzy")
+    assert results == []
+
+
+def test_search_invalid_query_returns_empty(tmp_pyra_home):
+    from pyra.memory import database
+    database.upsert("user/profile.md", content="Hello world.", category="user",
+                    modified="2026-05-18T10:00:00")
+    # FTS5 special chars that could raise OperationalError are handled gracefully
+    results = database.search('"unclosed quote')
+    assert isinstance(results, list)
+
+
+def test_migrate_from_files(tmp_pyra_home):
+    from pyra.memory.writer import write_memory
+    from pyra.memory import database
+
+    write_memory("user/note.md", "Migration test content.")
+
+    # Wipe DB to simulate fresh state before migration
+    database.remove("user/note.md")
+    assert database.list_all() == []
+
+    # Manually call migrate — it should re-populate from the .md file
+    database.migrate_from_files()
+    rows = database.list_all()
+    assert any(r["path"] == "user/note.md" for r in rows)
+
+
+def test_list_memories_uses_db(tmp_pyra_home):
+    from pyra.memory.writer import write_memory
+    from pyra.memory.reader import list_memories
+
+    write_memory("context/project.md", "# Project\n\nActive tasks.")
+    memories = list_memories()
+    names = [m.name for m in memories]
+    assert "context/project.md" in names
+
+
+def test_lookup_memories_uses_fts(tmp_pyra_home):
+    from pyra.memory.writer import write_memory
+    from pyra.memory.reader import lookup_memories
+
+    write_memory(
+        "knowledge/python.md",
+        "Python is a high-level programming language.",
+        summary="Python overview",
+        keywords=["python", "programming"],
+    )
+    results = lookup_memories("programming language")
+    assert len(results) >= 1
+    assert results[0]["file"] == "knowledge/python.md"