[permissions] Fix db reset leads to broken state if env var permission is not true

[ijreilly]

No description provided.

[Weiko]

LGTM

[greptile-apps]

PR Summary

This PR modifies the permissions feature flag handling to prevent broken states during database resets by moving control from database seeding to environment variable-based configuration.

• Removed IsPermissionsEnabled from default seeded feature flags in /packages/twenty-server/src/database/typeorm-seeds/core/feature-flags.ts
• Added conditional feature flag enablement in initPermissionsDev method in /packages/twenty-server/src/engine/workspace-manager/workspace-manager.service.ts
• Ensures permissions are only enabled when explicitly configured via environment variables

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