Added support for multiple samples in raw/

[ArtemSokolov]

If multiple images share the same markers and parameter settings, they can now be placed as subdirectories of raw/. In other words, instead of structuring the data as multiple projects:

image1/
  markers.csv
  params.yml
  raw/
    tile1.rcpnl
    tile2.rcpnl

image2/
  markers.csv
  params.yml
  raw/
    tile1.rcpnl
    tile2.rcpnl

they can be consolidated under the same project folder:

myproject/
  markers.csv
  params.yml
  raw/
    image1/
      tile1.rcpnl
      tile2.rcpnl
    image2/
      tile1.rcpnl
      tile2.rcpnl