feat(memory): add JSON index and runtime memory_lookup/read/write tools

Gives Pyra an active memory brain: memory_index.json tracks summary +
keywords per file (like an inode table), and three built-in tools let
the AI look up, read, and overwrite memory mid-session. write_memory
accepts summary/keywords; update_index() merges the JSON index without
losing existing metadata.

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

src/pyra/memory/writer.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from pyra.memory import _MEMORY_ROOT
-from pyra.memory.index import update_index
+from pyra.memory.index import update_index, update_json_entry
 from pyra.security.boundaries import assert_safe_path
 from pyra.utils.paths import safe_chmod
 
@@ -20,12 +20,20 @@ def _resolve_and_validate(name: str) -> Path:
     return path
 
 
-def write_memory(name: str, content: str) -> Path:
+def write_memory(
+    name: str,
+    content: str,
+    summary: str = "",
+    keywords: list[str] | None = None,
+) -> Path:
     path = _resolve_and_validate(name)
     path.parent.mkdir(parents=True, exist_ok=True)
     path.write_text(content)
     safe_chmod(path, 0o600)
     update_index()
+    if summary or keywords:
+        rel_key = path.relative_to(_MEMORY_ROOT).as_posix()
+        update_json_entry(rel_key, summary, keywords or [])
     return path