chore: preserve root worktree documents

docs/agents/domain.md

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+# Domain documentation
+
+ThothII uses a single domain context.
+
+## Before exploring
+
+Read:
+
+- `CONTEXT.md` for the canonical domain vocabulary;
+- relevant ADRs under `docs/adr/`, when present.
+
+Missing documents are not an error. Domain terms and ADRs are created only when an
+actual decision makes them necessary.
+
+## Vocabulary
+
+Use the canonical terms defined in `CONTEXT.md`. Avoid introducing synonyms for
+concepts already defined there.
+
+When a required concept is absent, use `domain-modeling` to clarify and record it.
+
+## Architectural decisions
+
+If proposed work contradicts an existing ADR, surface the conflict explicitly rather
+than overriding the decision silently.