Where can I find description of directory tree structure for L1C files (AUX_DATA, DATASTRIP, GRANULE, HTML, rep_info)?
The L1C products are the ortho-rectified top of atmosphere (TOA) reflectance products provided by the ESA SciHub. These are the input products of Sen2-Agri. Each L1C product is composed of 100x100km² tiles.
We can find the data structure of the L1C here
However, if you want to use the surface reflectance (e.g. to derive vegetation indices), you should use the L2A products, which are provided by Sen2-Agri system and stored under
/mnt/archive/l2a/. These products contains the surface reflectance products, i.e. the surface reflectance corrected from the effects of the atmosphere and provided along with masks indicating the status of each pixels: land, cloud, cloud shadows, snow, water, etc.
The format structure of the L2A products is provided in the MACCS installation package that you might have downloaded when doing the Sen2-Agri.