Keep the Atomic harness research notes

The ralph run's research stage mapped Atomic's SDK onto HarnessV1:
event translation, host tool round trips, the tool boundary, auth
modes, and caveats such as no cross-process resume and oversized tool
result truncation. Keep it with the branch so review can continue on
another machine.

The run was stopped during its first review round. Both reviewers had
no blocking findings; reviewer B noted one doc nit: self-hosting.md
names only ATOMIC_CODING_AGENT_DIR, but Atomic also honors legacy
PI_CODING_AGENT_DIR for the auto-mode auth.json path. The Docker build
could not be verified on this machine because its Docker Desktop network
fails TLS to registry.npmjs.org (npm.pkg.github.com and api.github.com
still work), so bun install inside the image cannot fetch the new
lockfile entries.

Assistant-workflow: ralph (run 0cfa5220-f488-43ef-8bb5-2f54cf5141f2)
Assistant-model: Claude Opus 5.5
Assistant-duration: 72m abandoned, estimated 90m
Assistant-verification: docker build unavailable: container TLS to registry.npmjs.org fails with UNKNOWN_CERTIFICATE_VERIFICATION_ERROR on this Docker Desktop host
User-preference: Stop the workflow and hand off when the local environment blocks verification; continue on another machine
Co-authored-by: Alex Lavaee <lavaman131@github.com>