HCS Parser: Create ome.tiff well by well

[SilinPavel]

This PR changes the way how we perform generation of OME.TIFF structure in HCS Parser. Previously we generated one big ome.tiff for each sequence, such file contains all wells related to the sequence. The Pros here is that we had more easy and flat structure, but also Cons of such approach is that during generation of very big ome.tiffs we could fail due to OOM errors, since such pictures requires a lot of memory to be generated.

New approach generate ome.tiff for each well in a sequence, it gives as more reliable systems, because, obviously such ome.tiff will require less memory to be generated.

This PR also includes changes regarding integrity check - during this check we validate that all pictures that are present in Index.xml file actually exists.