[Bug]: integration install/upgrade don't register extension commands for the new agent (only switch does)

[PascalThuet]

Bug Description

specify integration switch re-registers enabled extensions' commands for the target agent (register_enabled_extensions_for_agent). specify integration install and specify integration upgrade do not. integration.setup() only installs the integration's own core commands, not extension commands.

So when a second integration is added to a project, the new agent is missing the extension commands the first agent has (e.g. the bundled agent-context extension's /speckit.agent-context.update, and any other installed extension's commands).

Steps to Reproduce

1. specify init --here --integration claude
2. specify integration install codex
3. Inspect .specify/extensions/.registry: the agent-context entry's registered_commands contains only claude, not codex.

Reproduced on main @ 7106858:

registered_commands: { "claude": ["speckit.agent-context.update"] }

No codex key; codex has no rendered speckit.agent-context.update command.

Expected Behavior

Installing/upgrading an integration registers the enabled extensions' commands for that integration's agent, same as switch does — so every installed agent has the same extension commands.

Actual Behavior

Only switch registers extension commands for an agent. A second integration added via install (or refreshed via upgrade) never gets them, so its extension commands are silently absent.

Question for maintainers

The fix is to call register_enabled_extensions_for_agent(<agent>) from install and upgrade (as switch already does). Before I open a PR, one decision is yours:

Should install/upgrade register all enabled extensions for the new agent (full parity with switch), or only a subset?

• Full parity (recommended): every installed agent ends up with every enabled extension's commands. Consistent with switch; smallest, most predictable change. Downside: install/upgrade start writing more files than today.
• Subset / opt-in: narrower blast radius, but special-cases which extensions propagate to which agents — more config, easy to get inconsistent.

If full parity is fine, I'll send a PR adding the register_enabled_extensions_for_agent call to both paths with tests.

Code references (main @ 7106858)

• integrations/_migrate_commands.py — switch calls register_enabled_extensions_for_agent(target); upgrade does not.
• integrations/_install_commands.py — install does not call it.
• integrations/base.py — setup() installs the integration's own commands only.

Specify CLI Version

main @ 7106858

AI Agent

Codex CLI

Related: #2879 (multi-integration), #2881 / #2885 (agent-context back-fill — surfaced this gap but intentionally left it out of scope).

[mnriem]

Full parity as that would be the expectation