fix(core): preserve agent permission precedence

[rekram1-node]

Summary

• apply global permission rules as defaults before built-in agent policy and configured per-agent overrides
• prevent migrated legacy bash rules from re-enabling shell for Explore
• remove duplicate schema-default permission entries from built-in agents

Testing

• bun test --only-failures in packages/core (1259 passed, 6 skipped)
• bun typecheck in packages/core
• push hook repository typecheck (31 packages)