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Using ArcMap/ArcCatalog 10.2, is there a way, to summarize a huge number of widely spread shapefiles/sources (different servers, different hard drives etc.) into one centralized database, in order to be able to transfer this database as well as a corresponding mxd-file e.g. to a notebook or another computer without internet connection?

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This is very easily done by adding each of these data sources to a map and then Creating a map package:

Map packages (.mpk) make it easy to share complete map documents with others. A map package contains a map document (.mxd) and the data referenced by the layers it contains, packaged into one convenient, portable file.

The same functionality is also available in the Package Map (Data Management):

Packages a map document and all referenced data sources to create a single compressed .mpk file.

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