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Maintainer decision on #672: the app's Save As keeps TIFF layers as Photoshop does (it sets ExportOptions.tiff_layers from its Layers option), but scripted and agent saves stay flat by default so conversions keep predictable sizes. #672 merged with the default on, so every headless TIFF save became layered. - photocraft-io: ExportOptions::default() has tiff_layers: false. The desktop and web Save As already set it explicitly from their settings, so the app is unchanged. - photocraft-cli: --tiff-layers on convert, run and batch (listed in the usage text). - engine: file.saveACopy, Batch, Image Processor, the export-to-files commands and the lens batch take "tiffLayers": bool=false, through one SaveOpts { quality, tiff_layers }. - automation: serve doc.save and MCP doc_save take tiffLayers (default false). - Tests: default ExportOptions write a flat TIFF; the CLI writes flat without the flag and layered with it (run and convert); #672's layered-TIFF tests ask for layers explicitly. Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>