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Fix autopilot agents skills detection - #1
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…ectory Current spec-kit installs the Codex SDD phase skills natively under .agents/skills/<cmd>/SKILL.md (github/spec-kit#1906) instead of the legacy .codex/skills/ path. The autopilot preflight gate only looked in .claude/skills/ and .codex/skills/, so a fresh Codex install reported the phase commands as missing and the autopilot refused to start. Projects were working around this by hand-writing .codex/skills compatibility-marker stubs purely to pass the gate. Teach the gate to also accept .agents/skills/<cmd>/SKILL.md so no shims are needed. Adds a layer-4 test covering the .agents/skills layout. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
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