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Measurement units - The unit chosen here will be the primary unit used in rulers and the Info window. (Some text boxes in the Info window use these units; if you type a number into the box, it'll be assumed to use the units chosen here. You can type a unit abbreviation following the number, and it'll be automatically converted to the units chosen here. Valid abbreviations are in for inches, cm for centimeters, pt for points, and p for picas.)
On startup - OmniGraffle can automatically re-open any documents you had open the last time you quit it. You also have the option of automatically creating an Untitled document if no other documents are open already. Saving documents - By default, every document you save will be saved as a single file. If a document contains any images (or any shapes with an image fill), these images will be "serialized" and saved in the same file. However, this serialization process inflates the data size of the image, so it may not be desirable in all cases. If Save as file wrapper is chosen, the document will be saved as a "file wrapper" -- a folder containing the OmniGraffle data and any embedded images each as separate files, which appears in the Finder as a single document icon. (This is similar to the RTFD format for TextEdit documents.) File wrappers can also be difficult to work with, so you might not always want to use them either. You can have the best of both world by choosing Save as single file unless there are images; if this is chosen, documents containing images will be saved as file wrappers, and other documents will be saved as plain files. Shadows - The Draw shadows beneath everythihg else option allows you to achieve slightly more correct-looking output when documents are printed or exported to PDF. Text Editing, Line Creation, and Line Label Creation - These options allow you to configure keyboard and mouse behaviors for editing documents to whatever best suits your working style.
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