[refactor] remove dead code and get rid of gdal-bin and plyextrema

[carlodef]

List of changes:

• all system calls to GDAL cmdline tools (e.g. gdal_translate, gdalinfo, gdalbuildvrt, ...) are replaced with rasterio, which is easier to use from python
• the plyextrema C binary is removed and replaced with numpy functions
• some dead code is removed