fix: make knowledge_graph.py SQLite connections exception-safe

Wrap all 8 methods that open SQLite connections with
contextlib.closing() to guarantee conn.close() is called even if
execute()/commit()/fetchall() raises. Previously, connections would
leak on exception since close() was called manually after operations.

Add transaction context manager (with conn:) to write methods
(add_entity, add_triple, invalidate) for auto-commit on success and
auto-rollback on exception. Read methods use closing() only.
_init_db keeps manual commit since executescript has its own
transaction semantics.

Author: adv3nt3