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Apply the remediation from the bug assessment on issue #3990. After integration setup() and manifest.save(), when --force is used (re-initializing an existing project), call _register_presets_for_agent and _register_extensions_for_agent so that previously-installed presets and extensions are recomposed on top of the freshly-regenerated core files. Without this, preset-composed files reverted to pure core while the preset registry continued to report them as installed. This mirrors the same pattern already present in integration_upgrade() (added in PR #3853 / issue #3849 for the upgrade path). Refs #3990 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>