add update_project_soul tool for clearer soul updates

Models previously had to piece together that the soul = context.md +
conventions.md and call update_context twice with specific filenames.
New tool accepts context and/or conventions params in a single call.
Updated all tool descriptions, unfilled-soul messages, and docs to
reference update_project_soul as the primary way to populate the soul.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>