`hermes uninstall --gui` deleted hermes-agent/node_modules on the premise
that the workspace root only carries Electron. The root package.json is
an npm workspace (apps/*, ui-tui, ui-tui/packages/*, web, tests-js), so
the root node_modules holds the hoisted dependencies of the TUI and the
dashboard too, while Electron itself resolves from
apps/desktop/node_modules, which is still removed.
Stop treating the workspace root as a GUI artifact, list it under "Kept
intact" in the removal plan, correct the docstring and the desktop guide,
and add a regression test that a real `--gui --yes` removal keeps agent
data and the shared dependencies while removing every GUI artifact.
Refs: #128974
Salvaged-from: #131147
f9fec19d96