fix: remove agent manifest files from activation job sparse checkout (#26483)

* fix: remove agent manifest files from activation job sparse checkout

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/e0243bc9-3522-492d-91d7-6bfbab86eb35

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

* fix: keep engine-specific folders but remove root instruction files from activation sparse checkout

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/63afa6a2-c21a-4336-8c72-0c710bff9b26

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

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Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

Author: Copilot