Add secrets infrastructure: DB tables, shared types, env binding model, and migration improvements

Introduce company_secrets and company_secret_versions tables for
encrypted secret storage. Add EnvBinding discriminated union (plain vs
secret_ref) to replace raw string env values in adapter configs. Add
hiddenAt column to issues for soft-hiding. Improve migration system
with journal-ordered application and manual fallback when Drizzle
migrator can't reconcile history.

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

packages/adapter-utils/src/types.ts

@@ -129,6 +129,7 @@ export interface CreateConfigValues {
   args: string;
   extraArgs: string;
   envVars: string;
+  envBindings: Record<string, unknown>;
   url: string;
   bootstrapPrompt: string;
   maxTurnsPerRun: number;