Instead of opening another thread, I'll reply to this one as it is somehow related.
I installed Sen2Cor 2.0.6 on Ubuntu 14.04 LTS, as documented.
I downloaded 2A_OPER_PRD_MSIL1C_PDMC_20151201T182509_R137_V20151129T112140_20151129T112140.
After subsetting the scene, as it is a 6,3 GB full scene, using Sen2Cor give me the "fatal error" :
directory "..../DATASTRIP/" does not exist.
EDIT: From what I'm understanding, the ancillary mask data aren't being subset and copied.
I had to execute Sen2Cor on the full scene, for a 10 hour run, with the already reported warnings but with useful results.
Is there any method to subset or apply a mask to a full scene, before calibrating with Sen2Cor?