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Organize and name files meaningfully.
What makes sense for you:
Use file naming conventions for related files
Possible elements for file names:
Use open file formats for long term storage of data: Some file formats are less susceptible to obsolescence than others
Project- & folder-level
Use Readme Files
An Example of Readme file and metadata for a dataset in Dryad.
Readme file for this data
Metadata for the data set