When user selects "Skip research" during /gsd:new-milestone, the choice
was not saved to .planning/config.json. Later, /gsd:plan-phase would
read the default (research: true) and spawn researchers anyway.
- Add `config-set` command to gsd-tools.js for setting nested config values
- Update new-milestone workflow to persist research choice after user decides
Closes#484
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>