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[Enh] Harmonize how working directory is handled in Clinica.
[New] For any pipeline, delete automatically working directory if not specified in the CLI.
[Fix] Catch case when no image is given to a pipeline (e.g. because they were already processed in CAPS directory).
[Enh] Harmonize use of pipeline parameters and how they are handled.
Pipelines:
[Change] Pipeline classes associated to t1-volume and t1-volume-existing-template command lines are removed. They are simply replaced by successive calls of t1-volume* sub-pipelines.
[New] For t1-freesurfer, display failed images when an error occurs during the execution of the pipeline.
[New] For t1-freesurfer, add --overwrite-outputs flag. When used, images already run in CAPS directory will rewritten. Otherwise, they will be skipped before the execution of the pipeline.
[Fix] Remove mentions of modulation in t1-volume-parcellation arguments (modulated images are always chosen).
[Fix] Remove --smooth flag in t1-volume-tissue-segmentation (should not exist).
[Enh] (All pipelines) Remove discrepancy between CLI flag and pipeline parameter.