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A few days ago, Aaron Bartell posted a question regarding comparing source in an iSeries project to the version on the System i.
I just stumbled upon the fact that the RSE's built in compare function does this. If you have the local version of the source open, you can click the triangle icon in the workbench toolbar, or choose "Edit -> Compare to file ...". You can then choose the remote source with which to compare your local source.
This method of comparison has its own idiosyncrasies, just like the RSE Extensions version and Eclipse's "Compare with -> Each other". One of the big benefits of the RSE version is that you can use it to merge source without losing the sequence numbers / dates, but with an "undo" (unlike PDM option 55).
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