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Improve CLI interface to support --help or BrainGnomes help
Add CLI status command to get project status from command line
Add dry_run option to run_project to see what would be run without executing it
Refactor prefetch to accept cohort specifications and extend them to T2w fetch.
Refactor prefetch to fall back to no desc field if desc:brain fails
Expand fMRIPrep TemplateFlow defaults to include MNI152NLin2009cAsym boldref, res-2 brain mask, brain probseg, and carpet dseg assets observed during workflow construction
Add conditional CIFTI TemplateFlow defaults so prefetch only stages MNI152NLin6Asym and fsLR sphere assets when fMRIPrep CLI options request --cifti-output
Harden prefetch caching and validation checks so that later failures invalidate skip logic
Make prefetch state query-specific so that an exact snapshot of templateflow files is retained
Move prefetch state files out of templateflow_home and into hashed project log paths; legacy state files in templateflow_home are now migrated and removed to avoid poisoning TemplateFlow standard-space discovery.
Expand TemplateFlow default to desc=None for T1w to mirror some versions of fmriprep.
Harden check on flywheel location to accommodate missing fw command.
Update RSQLite connections to default to synchronous=NULL to prevent spurious warnings
Included OASIS30 as a default template space for prefetch because it is used by fmriprep
bugfix: preserve cohort-<n> in BIDS parsing/reconstruction so postprocessing can resolve cohort-qualified fMRIPrep outputs such as space-MNIPediatricAsym_cohort-2