PR #1318 — Hardening: Prohibit Direct todo.md Hand-Edits Across Harness Instruction Templates

The Broader Goal at the End of the Previous PR

PR #1316 shipped the automated live in-sandbox GitHub-write probe (TC-9, issue #1213), closing the empirical verification gap across the fleet. Following that landing, an audit of model behavior revealed a chronic reflex where dispatched agents across all harnesses repeatedly attempted to hand-edit project-docs/todo.md directly.

What Was Missing & The Real Root Cause

An audit of instruction templates in synlynk/instructions.py and active directive files (CLAUDE.md, GEMINI.md, GROK.md, .github/copilot-instructions.md, .windsurfrules) identified a direct contradiction:

• The instruction templates explicitly commanded agents to - Update task status in project-docs/todo.md ([ ] → [x]).
• In synlynk's runtime architecture, however, state.db is the authoritative single source of truth; todo.md is an auto-generated view projected at synlynk checkpoint, and _hc_todo_drift in synlynk doctor warns against manual hand-edits.

What Shipped

1. Instruction Template Hardening (synlynk/instructions.py):
   • Updated _session_protocol, _build_cursor_mdc(), _build_copilot_instructions(), and _build_windsurf_rules() to explicitly prohibit hand-editing todo.md and direct agents to use synlynk story done <id> (or synlynk story create/update) and synlynk checkpoint.
2. Directive Files Alignment:
   • Updated root directive files (GEMINI.md, CLAUDE.md, GROK.md) to eliminate legacy checkbox hand-edit instructions.
3. Unit Test Coverage (tests/test_instructions.py):
   • Added test_instruction_templates_prohibit_direct_todo_edits() asserting that all generated templates prohibit direct todo.md edits and reference state.db / synlynk story done / synlynk checkpoint. All 15 tests pass.