chore(docs): remove stale root-level docs

- SHUTDOWN_BUG_ANALYSIS.md: debug analysis, fix already shipped
- autonomous_summary.md: spec 042 agent report, spec already merged
- MANUAL_TESTING.md: references stale .tree/next worktree and pre-refactor terms
- docs/upstream-issue-draft.md: outdated mcp-go upstream issue draft

Also fix dangling MANUAL_TESTING.md links in docs/tray-debug.md and
docs/oauth-e2e-plan.md. References inside specs/007-oauth-e2e-testing/
preserved as historical spec artifacts.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: claude