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Troubleshooting

  • dotagents doctor is the first stop: it validates skill frontmatter, role definitions, lock pins, materialized copies, hook registration, and audits external sources.
  • Upgrading from an old config that targets agent pi with MCP: vanilla Pi has no MCP surface, so the target is ignored with a warning — rename pi to omp in dotagents.yaml if you meant the OMP fork.
  • A sync proposed removals you didn't expect: setup-driven syncs always preview removals per harness and default to keeping your files; answer n and inspect with dotagents status.
  • "exists but is not a symlink" conflict on a root instruction file: a real file occupies the harness's memory path (e.g. ~/.claude/CLAUDE.md). dotagents never overwrites it silently — migrate the content into ~/.agents/AGENTS.md, delete the real file, and rerun dotagents sync.
  • Memory tools skipped during sync: no Go toolchain on PATH. Install Go, or copy prebuilt binaries to $GOBIN/~/.local/bin manually; sync will manage them from then on (rebuilds only when sources change).