fix(memory): stop empty phase2 from wiping consolidated artifacts

[F0Rextasy]

What

I reviewed the full diff; every empty Phase 2 run deleted MEMORY.md, memory_summary.md, and skills even when live consolidations existed, so the empty-input path now advances its watermark without touching on-disk artifacts.

Why

Fixes #12596 (data-loss half; the case-variant scope-key half stays open for a follow-up)

Testing

• bun test packages/coding-agent/test/memories-runtime.test.ts (8 pass, 1 updated: empty Phase 2 preserves MEMORY.md/summary/skills)
• bun --cwd=packages/coding-agent run check:types (pass)
• oxlint + oxfmt on both changed files (pass)

---

• bun check passes
• Tested locally
• CHANGELOG updated with the required attribution (if user-facing; internal issue fixes use issue links, external contributions add the PR link and contributor credit after creation)

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