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* fix: register enabled extensions for agent on integration install/upgrade install and upgrade only set up the integration's own core commands; only switch re-registered the enabled extensions' commands for the target agent. A second integration added via install (or refreshed via upgrade) was therefore silently missing the extension commands the existing agents already had (e.g. the bundled agent-context extension). Extract switch's registration into a shared _register_extensions_for_agent helper and call it from install and upgrade too, so every installed agent ends up with every enabled extension's commands — full parity with switch. Closes #2886 * test: pin skills-mode secondary-agent registration; document #2948 limitation Extension skill rendering is scoped to the active agent (init-options track a single ai / ai_skills pair), so a skills-mode agent registered while not active (e.g. Copilot --skills installed as a secondary integration) gets command files rather than skills. install/upgrade match extension add here; only switch renders skills, because it activates the target first. Add a regression test pinning this behavior and document the limitation on the shared helper. Per-agent skills parity is tracked separately in #2948. * fix: don't re-render the active agent's skills when registering a non-active agent register_enabled_extensions_for_agent runs an active-agent-scoped skills pass (_register_extension_skills resolves the skills dir from init-options["ai"], ignoring the passed agent). Routing install/upgrade of a secondary integration through it re-rendered the *active* skills-mode agent's extension skills as a side effect — resurrecting skill files the user had deliberately deleted. Gate the skills pass on the target being the active agent; switch is unaffected because it activates the target first. Also harden the skills-mode install test (assert a core skill so --skills is load-bearing, drop a vacuous registered_skills assertion) and add a regression test. Surfaced by review of the PR; skills parity for non-active agents stays tracked in #2948. * refactor: share the extension-op scaffold and run (un)registration post-commit Review cleanups, no behavior change on the success path: - Extract the best-effort ExtensionManager scaffold (lazy import, instantiate, except -> _print_cli_warning) into _best_effort_extension_op. Both _register_extensions_for_agent and a new _unregister_extensions_for_agent delegate to it, removing the duplicate block left inline in switch. - Invoke the best-effort extension registration AFTER the install/switch/upgrade try/except has committed, so a failure in it can never trigger the rollback (install and switch teardown on except). * docs: clarify extension registration parity scope * fix(integrations): defer extension registration until use * fix(tests): remove redundant shutil import * fix(integrations): backfill extensions for installed switch targets