Multi-repo on v2: the setup script runs once in the worktree container instead of in each repository #343

On v2 multi-repo (#338), an isolated run of a multi-repo workspace runs the project's setup script once, in the container folder, with T3CODE_REPO_ROOT unset. A script written for a repository skips every repository. cp "$T3CODE_REPO_ROOT/.env" . fails with cp: /.env: No such file or directory and the run stops at "Workspace preparation failed". The pre-v2 branch ran it per repository (#328, #329).

Expected: the script runs once per repository, in that repository's worktree, with T3CODE_REPO_ROOT set to the checkout it came from. Setup output carries the repository name, each repository gets its own terminal, and a failure names the repository.