Add --prune flag to seed command to remove stale data

Without --prune, seeds continue to only upsert (add/update).
With --prune, routes, encounters, and bosses not present in the
seed JSON files are deleted from the database.

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

.beans/nuzlocke-tracker-ecn3--prune-stale-seed-data-during-seeding.md

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+---
+# nuzlocke-tracker-ecn3
+title: Prune stale seed data during seeding
+status: completed
+type: bug
+priority: normal
+created_at: 2026-02-21T16:28:37Z
+updated_at: 2026-02-21T16:29:43Z
+---
+
+Seeds only upsert (add/update), they never remove routes, encounters, or bosses that no longer exist in the seed JSON. When routes are renamed, old route names persist in production.
+
+## Fix
+
+After upserting each entity type, delete rows not present in the seed data:
+
+1. **Routes**: After upserting all routes for a version group, delete routes whose names are not in the seed set. FK cascades handle child routes and encounters.
+2. **Encounters**: After upserting encounters for a route+game, delete encounters not in the seed data for that route+game pair.
+3. **Bosses**: After upserting bosses for a version group, delete bosses with order values beyond what the seed provides.