docs: stale memory-bank references in tests and the phase protocol

[TKaltofen]

Summary

Three references point at memory-bank paths that do not exist, two of them from before the memory bank was slimmed to two files (PR #877).

Motivation

Agents and contributors treat these paths as real; each is a small trap.

Code pointers

• tests/README.md:30 lists a test_memory_bank/ directory that does not exist under tests/.
• tests/test_core/test_setup/test_link_on_methods.py:25 references /memory-bank/design-decisions/joinspec-convenience-function.md, which does not exist on main.
• CLAUDE.md and AGENTS.md (Phase Completion Protocol) reference memory-bank/todo.md; the file only exists transiently during phased work, which now reads oddly next to the two-file Memory Bank section. Clarify or drop.

Definition of done

The two dead paths are removed or corrected, and the todo.md mention is either clarified as transient or removed, with CLAUDE.md and AGENTS.md kept in sync.