Run 'make clean' on subdirs before removing 'dist/'.
Disable importing 'ijpy' as it has to be run from within Fiji.
Create target directory structure for jar.
Minor comment change.
Makefile integration for 'auto_run'.
Makefile integration for 'scripts'.
Add optional boolean argument 'runparser'.
Remove documentation of old datastructure, not used anymore.
Add find_mosaictrees().
Split mosaic parsing into single parser and wrapper methods.
Fix control flow on broken subvolumes.

The previous implementation did not stop processing the subvolumes if one of
them was broken, but continued with the next one of the dataset. This was never
an issue until we came across an experiment where one mosaic had some missing
subvolumes, but later ones were present. In that case the code was trying to
add them as subvolume, whereas the dataset itself had been set to "None"
already (which caused an exception then).
Print 'no valid mosaics' warning also to IJ log.