Group fields from configuration.json into different categories

[Shettland]

In order to organize the contents of configuration.json, some fields can be grouped into different categories depending on the tools that use them. For example, the last change was made to group every field used in sftp_handle.py into the key "sftp_handle", which makes it more obvious for the reader to understand where are these fields being used and what for.

The rest of the fields could be organized into "general" or "other", following the next structure:

{
   general: {
       ...
   }, 
   read_metadata_lab{
       ...
   },
   sftp_handle: {
       ...
   },
   ...
}