feat(memory): wire database into reader, writer, and bootstrap

- reader: list_memories() queries memory_meta; lookup_memories() uses FTS5 with
  fallback to JSON index substring search
- writer: write_memory() and append_memory() upsert to DB after every file write
- dirs: bootstrap() calls init_db() + migrate_from_files() on startup

Existing .md files remain the canonical store; SQLite is the search index.

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

src/pyra/memory/writer.py

@@ -1,3 +1,4 @@
+import datetime
 from pathlib import Path
 
 from pyra.memory import _MEMORY_ROOT
@@ -20,6 +21,25 @@ def _resolve_and_validate(name: str) -> Path:
     return path
 
 
+def _upsert_to_db(path: Path, content: str, summary: str = "", keywords: list[str] | None = None) -> None:
+    from pyra.memory import database
+    if not database._DB_PATH.exists():
+        return
+    rel = path.relative_to(_MEMORY_ROOT).as_posix()
+    category = rel.split("/")[0] if "/" in rel else "root"
+    stat = path.stat()
+    mtime = datetime.datetime.fromtimestamp(stat.st_mtime).isoformat(timespec="seconds")
+    database.upsert(
+        rel,
+        content=content,
+        category=category,
+        size_bytes=stat.st_size,
+        modified=mtime,
+        summary=summary,
+        keywords=keywords,
+    )
+
+
 def write_memory(
     name: str,
     content: str,
@@ -34,6 +54,7 @@ def write_memory(
     if summary or keywords:
         rel_key = path.relative_to(_MEMORY_ROOT).as_posix()
         update_json_entry(rel_key, summary, keywords or [])
+    _upsert_to_db(path, content, summary, keywords)
     return path
 
 
@@ -42,9 +63,12 @@ def append_memory(name: str, content: str) -> Path:
     path.parent.mkdir(parents=True, exist_ok=True)
     if path.exists():
         existing = path.read_text()
-        path.write_text(existing.rstrip() + "\n\n" + content)
+        new_content = existing.rstrip() + "\n\n" + content
+        path.write_text(new_content)
     else:
-        path.write_text(content)
+        new_content = content
+        path.write_text(new_content)
     safe_chmod(path, 0o600)
     update_index()
+    _upsert_to_db(path, new_content)
     return path