0.8

• Add optional low-pass filtering of motion parameters before FD recomputation; rename notch config fields to
  bandstop_min_bpm/bandstop_max_bpm (deprecated: band_stop_min/band_stop_max).
• All HPC jobs are now tracked in detail by an SQLite database
• Job failures and other errors can now be investigated using diagnose_pipeline
• Added a new vignette, "Diagnosing Pipeline Runs", that walks through get_project_status(), get_subject_status(),
  and interactive use of diagnose_pipeline()
• Improved error logging in HPC scripts so that success and failure are indicated more clearly
• Stale .fail files are removed when a newer .complete file exists, clarifying status of processing steps
• Jobs now write a manifest of files and times to the job tracking database for more thorough completeness tests
• Added optional low-pass filtering of motion parameters, matching Gratton
• Gracefully adjust motion filtering parameters if they fall above Nyquist at this TR
• Modify extract ROIs config to avoid input_regex and always generate it internally from postproc stream
• Add optional header row for postprocessed confounds TSVs, configurable via postprocess YAML and validated during setup
• Added extensive checks on write/permission issues with directories and files
• bugfix: Get CSF probseg image for MRIQC during prefetch
• run_project() now skips TemplateFlow prefetch only when a prior successful prefetch covers requested spaces and the TemplateFlow manifest in job tracking still verifies; missing/deleted template files trigger re-prefetch.
• bugfix: preserve user-specified metadata/log_directory (including external paths) instead of always resetting to <project_directory>/logs.
• During postprocess setup, confound_calculate now offers guided prompts to add framewise_displacement when omitted, including whether to use motion-filtered FD and whether FD should be processed vs kept as noproc for QC/exclusion workflows.
• Increase consistency of instructions and formatting in setup_project()
• bugfix: avoid spurious "Already disconnected" warnings on exit from diagnose_pipeline()
• bugfix: diagnose_pipeline() now respects configured metadata/log_directory instead of assuming <project_directory>/logs
• bugfix: diagnose_pipeline() now matches subjects by exact sub-<id> tokens to avoid accidental partial matches
• bugfix: run_bg_and_wait() now suppresses and restores ERR trap handling around wait, so non-zero container exits can be reconciled against success tokens before jobs are marked failed.
• bugfix: shell trap handlers now attempt a best-effort SQLite status update to FAILED before exit, reducing _fail/DB mismatch after abrupt failures.
• bugfix: update_tracked_job_status() now warns when no tracking rows are updated for a job_id (instead of failing silently).
• bugfix: check_status_reconciliation() now checks .fail markers against DB status and reports mismatch details.