docs: remove stale memory-bank references and clarify the transient todo.md

[dchaudhari7177]

All three references from the issue, each verified against main before touching it.

1. tests/README.md — test_memory_bank/

The layout tree listed a test_memory_bank/ directory. There is no such directory under tests/. Removed the line.

2. test_link_on_methods.py — dead design-decision path

The module docstring's See Also pointed at /memory-bank/design-decisions/joinspec-convenience-function.md. Neither that file nor the memory-bank/design-decisions/ directory exists on main.

Dropped that line and kept GitHub Issue #133: JoinSpec Convenience Function, which still resolves — so the docstring keeps a working pointer to the rationale rather than losing the context entirely.

3. todo.md in the Phase Completion Protocol

The protocol read as though memory-bank/todo.md were a standing file, which sits oddly next to the slimmed Memory Bank section.

I clarified rather than dropped it: the protocol itself is still used, it's only the file's status that was unstated. Both files now say up front that todo.md is transient — created for the duration of a phased task, removed when the work lands, and therefore not one of the Memory Bank core files — before listing the steps.

CLAUDE.md and AGENTS.md are kept in sync (I diffed the two sections to confirm they're identical).

Note on overlap

This deliberately avoids the Memory Bank / core-files section that #877 is rewriting — the only shared files are CLAUDE.md/AGENTS.md, and this change is confined to the Phase Completion Protocol section, which #877 doesn't touch. So the two should merge cleanly in either order.

I did not touch #873's two catalog files, since #877 already removes them.

Checks

ruff format --check --line-length 120 (597 files already formatted) and ruff check both clean; tests/test_core/test_setup/test_link_on_methods.py — 18 passed. Docs/comments only, no behaviour change.

Closes #878