When the M3C2 plugin is run through command line, cloud#1 is always subsampled to generate core points, even with SubsampleEnabled=false.
I ran the GUI plugin, saved the parameters file, ran the same thing though command line and got a different output (subsampled cloud)
M3C2 command line subsample
Re: M3C2 command line subsample
Which version are you using? I believe this bug has been fixed recently (i.e. in the 2.11.alpha version)
Daniel, CloudCompare admin
Re: M3C2 command line subsample
OK great, I'm using 2.10.2