fix: address third round of review feedback (multi-integration semantics)

Fixes five deeper active-only registration bugs surfaced by Copilot review
after 2486c08, all in the presets/extensions single-active integration
rule (#2948):

1. presets: _reconcile_composed_commands (run after install/remove)
   bypassed the active-only filter entirely, writing composition-winner
   command files for every detected non-skill agent via
   register_commands_for_non_skill_agents. Added an only_agent param to
   that registrar method (mirroring register_commands_for_all_agents)
   and threaded it through all 5 reconciliation call sites.

2. presets: `integration use copilot` with --skills (ai_skills: true)
   wrote both the static .agent.md command file AND the SKILL.md
   mirror for the same override. Mirrored the extension path's
   ai_skills guard in both _register_commands and the reconciliation
   pass: a command-backed active agent running in skills mode is
   excluded from non-skill command registration.

3. presets: registered_skills was a flat list, so switching between
   two skill-mode agents (e.g. Claude -> Codex) and then removing the
   preset only restored the currently active agent's directory,
   permanently orphaning the other. _unregister_skills now restores
   every existing skill-mode agent directory instead of only the
   active one.

4. extensions: load_init_options() collapses "no file" and "corrupted
   file" into the same {}, so the round-2 fail-closed fix didn't
   actually distinguish them. Added a shared
   resolve_active_agent_for_registration() helper in _init_options.py
   that checks file existence separately from parse success, returning
   a distinct sentinel for "file absent" vs None for "corrupted or
   invalid". extensions/__init__.py now uses this helper.

5. presets: same corruption-collapsing bug in _register_commands's
   active_agent resolution. Now uses the same shared helper as (4).

Adds regression tests for all five: reconciliation active-only
filtering, copilot --skills dual-write prevention, multi-skill-agent
switch+remove, and corrupted init-options fail-closed behavior for
both extension add and preset add. Each test was verified to fail
against the pre-fix code and pass with the fix.

Targeted (883) and full (3923 passed, 109 skipped) suites pass; ruff
check clean.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

tests/integrations/test_integration_subcommand.py

@@ -1490,6 +1490,41 @@ class TestIntegrationInstall:
             "back-fill every detected agent (#2948)"
         )
 
+    def test_extension_add_corrupted_init_options_file_fails_closed(self, tmp_path):
+        """A present-but-unparseable init-options.json must fail closed too,
+        not be treated the same as "no file at all".
+
+        ``load_init_options`` returns ``{}`` for a corrupted/unreadable
+        file just like it does for a missing file, so a naive "no active
+        agent recorded" check based on ``load_init_options`` alone can't
+        tell a legacy pre-init-options project (legitimate all-agent
+        fallback) apart from a corrupted-but-present file for a #2948
+        project (must fail closed). Corrupting the file after a normal
+        init must not reintroduce the all-agent fallback.
+        """
+        project = _init_project(tmp_path, "claude")
+
+        result = _run_in_project(project, [
+            "integration", "install", "codex",
+            "--script", "sh",
+        ])
+        assert result.exit_code == 0, result.output
+
+        init_options_path = project / ".specify" / "init-options.json"
+        init_options_path.write_text("{not valid json", encoding="utf-8")
+
+        result = _run_in_project(project, ["extension", "add", "git"])
+        assert result.exit_code == 0, f"extension add failed: {result.output}"
+
+        registry_path = project / ".specify" / "extensions" / ".registry"
+        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
+            "extensions"
+        ]["git"]["registered_commands"]
+        assert registered == {}, (
+            "a corrupted init-options.json must fail closed, not be "
+            "treated like a legacy project missing the file entirely (#2948)"
+        )
+
 
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