Automatic reading of calibration from .tif files

Now recongnizes only first .czi file and fixes first job bug

This reverts commit fe74d067.

Conflicts:

	spim_registration/timelapse/Snakefile

Rule registration depends on the output of hdf5_xml and resave_hdf5
Protects it against too early deletion.

This approach assumes that the processing itself runs without error.
When Fiji fails in on process then the whole workflow needs to restart.
Because the dummy files are now gone.

Now uses sysconfcpus and cluster.jason is adjusted for these parameters

* added new function that replaces occurrences of a defined set of parameters
  (required to handle brackets inside filenames)
* using glob_and_escape in Snakefile now

Pipeline tested and works with single channel data

the output rule now references to the correct xml filename

Log files are ordered

hdf5_xml_output rule does again touch the output
Tested and works