#931 Agent setup suggests repo init in already initialized repos

Summary

In an already initialized swamp repository, swamp agent setup should not suggest running swamp repo init --tool pi to set up the repo. That guidance is misleading because the repo already exists.

Expected behavior

When the current directory is already initialized as a swamp repo and the user wants to enable the Pi agent integration, the suggested command should be:

swamp repo upgrade --tool pi

The message could say:

Run swamp repo upgrade --tool pi to use pi agent with this repo.

Actual behavior

The setup guidance suggests:

swamp repo init --tool pi

with wording like:

Run swamp repo init --tool pi to set up this repo.

Impact

This can confuse users and points them at the initialization path instead of the repository upgrade path for an existing repo.

Suggested fix

Detect when the repository is already initialized and switch the guidance from repo init to repo upgrade for adding the Pi agent tooling.