Add secrets documentation and inline env migration script

Document secret storage in DATABASE.md and DEVELOPING.md. Update
SPEC-implementation with company_secrets schema and indexes. Add
migrate-inline-env-secrets script for converting existing plain
env values to managed secrets (dry-run by default, --apply to commit).

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

package.json

@@ -13,6 +13,7 @@
     "test:run": "vitest run",
     "db:generate": "pnpm --filter @paperclip/db generate",
     "db:migrate": "pnpm --filter @paperclip/db migrate",
+    "secrets:migrate-inline-env": "tsx scripts/migrate-inline-env-secrets.ts",
     "db:backup": "./scripts/backup-db.sh",
     "paperclip": "node cli/node_modules/tsx/dist/cli.mjs cli/src/index.ts"
   },