fix: render extension skills for target agent, not just active agent …

[Nimraakram22]

Fixes #2948.

Problem

Extension skill rendering was scoped to the active agent (init-options.json's ai field) even when registering extensions for a different, non-active agent — e.g. after specify integration install copilot --integration-options "--skills" while Claude remained active, or specify integration upgrade copilot. The target agent received command files instead of SKILL.md files.

Root cause

ExtensionManager._get_skills_dir() and _register_extension_skills() always resolved the skills directory/settings from the active agent in init-options.json, ignoring the agent_name argument passed to register_enabled_extensions_for_agent().

Fix

• Added is_agent_skills_enabled() to resolve per-agent skills-mode from .specify/integration.json's integration_settings[agent].parsed_options.skills, falling back to the legacy global ai_skills flag for the active agent.
• Threaded agent_name through _get_skills_dir() and _register_extension_skills().
• register_enabled_extensions_for_agent() now computes skills_mode_active per the target agent, and always attempts skill registration for that agent (matching prior best-effort error handling).

Testing

• Manually verified: specify integration upgrade copilot --force with a non-active, skills-mode Copilot integration now renders .github/skills/speckit-git-*/SKILL.md files instead of command files, with no regression to the active agent's own skills.
• pytest tests/ -k extension: 616/616 pass.
• Full suite: 44 pre-existing failures unrelated to this change (Windows symlink-privilege and PowerShell path-resolution issues — confirmed present on main without this change).

[Copilot]

Pull request overview

Makes extension skill rendering aware of the target integration rather than only the active agent.

Changes:

• Resolves per-agent skills mode from integration state.
• Threads target agent through skill-directory resolution and rendering.
• Updates extension re-registration behavior and documentation.

Show a summary per file

File	Description
src/specify_cli/_init_options.py	Adds per-agent skills-mode resolution.
src/specify_cli/extensions/__init__.py	Targets extension skill generation by agent.
src/specify_cli/integrations/_helpers.py	Updates registration behavior documentation.

Review details

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Comments suppressed due to low confidence (2)

src/specify_cli/extensions/init.py:980

• The target-agent branch bypasses the repository's safe directory creation. resolve_agent_skills_dir only constructs a path, and _ensure_usable follows symlinked parents with mkdir; _register_extension_skills then writes SKILL.md beneath it. A project with (for example) a symlinked .github/skills can therefore make registration write outside the project. Route this path through _ensure_safe_shared_directory as resolve_active_skills_dir does (see shared_infra.py:163-196) before writing.

                skills_dir = resolve_agent_skills_dir(self.project_root, agent_name)

src/specify_cli/extensions/init.py:1856

• registered_skills is still a single global list of names, so merging a second agent's identically named skills loses which directories own them. For example, after Claude and non-active Copilot both render speckit-git-feature, uninstalling either agent removes its copy and clears the list in unregister_agent_artifacts; the other copy remains but is no longer tracked, so later extension removal leaves it orphaned. Track generated skills per agent (with legacy-list compatibility) before enabling multi-agent skill rendering.

                        existing_skills = self._valid_name_list(
                            metadata.get("registered_skills", [])
                        )
                        merged_skills = list(
                            dict.fromkeys(existing_skills + registered_skills)

• Files reviewed: 3/3 changed files
• Comments generated: 2
• Review effort level: Medium

[mnriem]

Please address Copilot feedback and address test & lint errors

[Nimraakram22]

@mnriem Thanks for the review! Pushed a follow-up commit addressing both points:

• Copilot's extension add gap: install_from_directory() now uses a new _register_extension_skills_for_installed_agents() helper that renders skills for the active agent and every agent in .specify/integration.json's installed integrations that has skills mode enabled — not just the active one. Verified manually: specify extension add git with Claude active + Copilot installed in --skills mode now reports "5 agent skill(s) auto-registered" and creates SKILL.md files under both .claude/skills/ and .github/skills/.
• Test coverage: added TestNonActiveAgentSkillRegistration (3 tests) covering the non-active-agent upgrade path, isolation from the active agent's own skills, and the extension add multi-agent path.

Also had to fix a regression this exposed: my agent-specific _get_skills_dir() branch was resolving the naive per-agent directory without the same symlink/containment/is-a-directory safety checks that resolve_active_skills_dir() applies for the active agent this broke the Hermes marker-file detection test, now fixed to mirror that logic exactly.

pytest tests/ -k extension: 619/619 pass. git diff --check: clean.