chore: preserve root worktree documents

docs/agents/issue-tracker.md

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+# Issue tracker: GitHub
+
+Issues and specifications for this repository live in GitHub Issues. Use the `gh` CLI
+for all operations.
+
+## Repository
+
+- Repository: `mptyl/ThothII`
+- URL: https://github.com/mptyl/ThothII
+- Pull requests as a triage surface: no
+
+## Conventions
+
+- Create issues with `gh issue create`.
+- Read issues and comments with `gh issue view`.
+- Apply labels with `gh issue edit`.
+- Record resolutions in a comment before closing an issue.
+- Refer to issues by their linked title in user-facing documentation, not only by
+  number.
+
+## Wayfinding operations
+
+- A Wayfinder map is an issue labelled `wayfinder:map`.
+- Decision tickets are child issues labelled `wayfinder:research`,
+  `wayfinder:prototype`, `wayfinder:grilling` or `wayfinder:task`.
+- Use native GitHub sub-issues and issue dependencies when available.
+- If native sub-issues are unavailable, use a task list in the map and add
+  `Part of #<map>` to each ticket.
+- If native dependencies are unavailable, add `Blocked by: #<issue>` to the ticket.
+- An open, unassigned and unblocked child issue belongs to the frontier.
+- Claim a ticket by assigning it before beginning work.
+- Resolve a ticket by recording the decision in a comment, closing it and adding a
+  linked one-line summary to the map.