spm rewrites headers on these files

in some workflows, you want to use the files with the modified headers,
not resliced images. So we'll just return the in_files in the output.
See SPM doco Chapter 2: Realign FMI:
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf
enable list of list of files from slice time output

looks like the variable 'run' never gets used… perhaps a typo.

output spec needed adjustment to handle list of lists.
fix indents - nothing real
normalize can take a list of lists of files as input.
make the point of this var more clear.
in_files -> modified_in_files

also fixes an embarassing if clause, and sets realigned_files to in_files if jobtype is "estimate"
Merge pull request #691 from beOn/spm_preproc

spm preproc fixes and adds