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Can I fix a CTM built repo with CVSup?



I keep a local repo via CTM.  I was having trouble with the server
crashing, so I bought a new disk drive (and ATA 100 controller :). 
Anyhow, I rebuilt the repo from the CTMs I had, but something seems 
amiss.  There are some files that shouldn't be there, or are just old.
In particular, ports/audio/libao/{{patches/{patch-src_Makefile_in,
patch-src_plugins_Makefile_in,patch-src_plugins_esd_Makefile_id,
patch-src_plugins_sun_Makefile_in},pkg/{PFRAG.arts,PFRAG.esd,PFRAG.sun}}
There may be more, but these are the ones I noticed.

I can fix my sources with 'cvs up' from a mirror, but how to fix the repo
itself?  I looked at CVSup, and it seems like it would do the trick,
but would that cause future problems, if I keep patching the repo with
CTMs?

Is this perhaps fallout from openbsd.org's network trouble?

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