fix: preserve registered integration skills during extension update

[chelsealong]

Description

Fixes #5002. Updating an extension now refreshes commands and native skills for integrations recorded in its previous registry entry, including a non-default Codex integration. An integration with no prior registration remains untouched.

Testing

• Regression test: failed before the fix because the Codex SKILL.md was deleted; both positive and negative cases pass after the fix.
• .venv/bin/python -m pytest tests/specify_cli/extensions/test_command_update.py tests/specify_cli/extensions/test_command_update_transaction.py tests/specify_cli/extensions/test_command_update_artifacts.py -q — 61 passed.
• .venv/bin/specify --help and git diff --check — passed.
• Ruff reports 20 findings in the touched files; the unchanged files report the same 20 findings.

AI Disclosure

• I used AI assistance.

AI disclosure: Codex (GPT-6, autonomous mode) investigated the issue and generated the code and regression test. No human review is claimed.