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Hello,
I understand why the layout settings files (e.g. omega/omega/layouts/simple/simple.layout.inc) are .inc rather than .info: so they won't be picked up by system_rebuild_theme_data(), however this causes a problem with code validation tools (like coder module) as .inc are supposed contain valid php code.
Since these are .inc and .inc are defined by drupal coding standards as to be php , these need to be run through exec() in omega_layouts_info()