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I have 2 naming standards files from ERwin (.nsm extension), and I want to compare them to see if they contain the same rules. Is there some sort of automated way to check this?

If there isn't a way to compare the two within ERwin itself, is there a way to convert the 2 files into a more 'standard' file type (i.e. an Excel file), and then compare the files that way? I'm coming from a programming perspective (mostly Java), and from what I've seen it wouldn't be that hard to write a program that compares 2 Excel files.

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Export both files, see How do I open an ERwin Naming Standards file (.nsm) in Excel?

Use a file compare tool to compare the contents.

If you decide to write a program yourself, follow the advice in this Stack Overflow answer:

Comparing the contents of 2 excel files

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