I have a question about l2gen output file. In the L2 netcdf output file I see longitudes slon, clon, and elon. And similar for latitude. I use clon and clat of each pixel as geolocation of that pixel when using in calculations. Is this a correct assumption?
There is no consistent method to identify clouds in L1 data. For the three missions you're interested in, there is some hope, though....
OLCI includes a qualityFlags.nc file that has, among others, a flag for "bright" targets.
OLI are TIFF images, but does include a "BQA" image that includes a bit for clouds
MSI are JPEG2000 images, but also include in the directory a subdirectory under "GRANULE" called QI_DATA that includes a set of XML files with flag information....good luck with that...