I am getting whole-file conflicts where the only difference is the
presence of ^M's in one version and not in the other.

Does this have to do with how the end-of-file setting is set in cygwin?

We have unix/linux clients and windows clients (with cygwin).  Cygwin
and non-cygwin tools are used to edit files (i.e., tools which put ^M's
into the files).

How can I avoid whole-file conflicts?

I am using the latest version of cygwin as of 11/2x/2000.

cc

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