tileIndex format is very restrictive

[raacampbell]

The tileIndex file links the TIFF tile names to a position in the sample. However, the format of this file only makes sense for data generated by orchestrator. Other acquisition systems won't produce data this way. The format only handles three channels.

We likely need a new tile index system that is a .mat file and is more flexible. This was already done for the tileStats files, but that was easier because we weren't using these files for anything until recently.

Maybe we could retain the old tileIndex system somehow as a legacy format and keep functions to hand that will handle this. Mark these as legacy and slowly phase them out.

[raacampbell]

We no longer need this and should remove all traces of it. Remove the requirement for the file to present from tileLoad (6499f21) and from stitchAllChannel (2bad3b4). It's still there in in syncAndCrunch, though, as generateTileIndex is used there to report how many tiles are present in the section acquisition directory.

[raacampbell]

See #173