repo sync duplicate path issue

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I've been building cyanogenmod for the oneplus one for a while now and I've replaced the stock kernel with boeffla kernel howerver i ran into an issue as of today (was able to repo sync with new kernel just fine before) All it says now when I do repo sync is :

fatal: duplicate path kernel/oneplus/msm8974 in /home/noahvt/BuildServer/Settings/.repo/manifest.xml

I check the manifest and just as I thought, it's not there... nor is it in default.xml there is only one in roomservice.xml which links to the custom kernel like so:

<project name="andip71/boeffla-kernel-cm-bacon" path="kernel/oneplus/msm8974" revision="boeffla_v5_cm" />

Can I make this thing forget the stock kernel because this keeps stopping me from doing a repo sync

Thanks

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Have added your device specific path in local_manifest.xml. If yes, then try to delete local_manifest.xml file instead add them to /.repo/local_manifest/roomservice.xml.