Perforce: Unable to resolve files manually in one shot

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After doing merge/integrate through branch mapping, several files are pending for manual resolve before I can submit the pending changelist. Now, the tool is telling me to "Resolve Files" one at a time and every time I am selecting "accept source" and doing auto-resolve.

Why the tool is not showing all the files which require manual resolve in one shot? Is there any command which I can use to do this?

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It's not clear which tool you mean, when you say "Why the tool is not showing all the files".

But, to answer your second question ("Is there any command which I can use to do this?"), you can run p4 resolve -ay to perform "accept yours" on all the files needing resolve.

You can also run p4 resolve -at to perform "accept theirs", p4 resolve -am to perform "accept merged", and p4 resolve -as to "accept safe".

For more information: https://www.perforce.com/perforce/r15.1/manuals/cmdref/p4_resolve.html

If you're not sure which option to use, try p4 resolve -as first, and then see if you have any files left which p4 resolve didn't know how to resolve safely.