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Feature: rework out_app_flag as a three-mode output controller with unified output directories, append semantics, and provenance headers - #8159

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mohanchen:2026-10-16-b
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Feature: rework out_app_flag as a three-mode output controller with unified output directories, append semantics, and provenance headers#8159
mohanchen wants to merge 65 commits into
deepmodeling:developfrom
mohanchen:2026-10-16-b

fix(input): create mode-2 subdirectories for out_hsr/out_pchg/out_wfc…

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