1.0

• Preserve integer NIfTI storage types after interpolation, regression, and
  filtering. Recalculate slope and intercept from the processed range and round
  to the output grid, avoiding fractional-value truncation, constant-output
  scaling failures, clipping, and narrowing integer intermediates. Reserve
  RNifti's INT32 missing-value code and reject non-finite integer output before
  writing a file. Regression tests cover all eight integer types, NIfTI-1/2,
  input scaling, expanded ranges, zero backgrounds, and extreme values.

• Decode integer images into double-precision working buffers and preserve
  FLOAT64 results without an intermediate FLOAT32 cast. This retains small
  differences at large offsets and supports NIfTI-2 scaling outside FLOAT32's
  range. Integer working buffers use twice the memory of the previous FLOAT32
  buffers; conversion temporaries are now freed instead of leaked.

• Suppress RNifti pointer/reference-count diagnostics in all native image
  helpers, including debug builds where pkgbuild overrides -DNDEBUG.
  Preserve normal BrainGnomes logging and other debug settings. Cleanly rebuild
  the package and create new runtime bundles to update future workers; existing
  sealed bundles retain their installed binary.

• Correct spline interpolation when retained timepoints are constant:
  censored spikes and edge samples now receive the retained value. Reject
  non-finite interpolation points explicitly.

• Apply fitted regression models to censored volumes even when fitted rows are
  constant. Respect partial regression that retains the intercept, including
  constant input series. Recenter residuals over fitted rows before applying
  a requested nonzero mean in both image and matrix regression.

• Support scalar-gain filters without invalid memory access, including
  steady-state initialization. Validate empty/non-finite coefficients and
  padding before processing, including all-zero images. Filter and demean
  nonzero constant signals when requested.

• Reject images with extra dimensions instead of silently processing their
  first block, and use size-safe voxel indices in native image operations.

• Reject missing regression selections, non-finite designs, and non-finite
  retained quantile voxels with clear errors. Quantiles continue to permit
  non-finite values outside a supplied mask.

• Detect configuration changes inside unnamed, mixed-name, and duplicate-name
  lists so confirmed saves retain those edits.

• Allow SQLite reads for job status, project inspection, submission history,
  and table existence to wait up to ten seconds for concurrent writers rather
  than failing immediately while a worker publishes its state.

• Correct menu titles and single-choice selection indices. Reject partial
  numeric choices and exit menu loops on EOF. Escape, Ctrl+D, and EOF cancel
  typed prompts cleanly and restore terminal settings. Cancelling guided
  stream selection stops before submission instead of selecting every stream.

• Preserve negative CLI values, empty assignments, and trailing equals signs.
  Keep leading zeros in subject/session identifiers and reject invalid boolean
  options before acting.

• Preserve literal shell-quoted paths containing spaces or apostrophes across
  CLI plans/setup/validation and worker entry points, while retaining vector
  option parsing.

• Parse complete BIDS filename entities instead of incidental substrings, and
  preserve alphanumeric resolution labels when constructing filenames.

• Validate motion-filter flags and require finite motion-QC thresholds before
  summarization.

• Document CLI activation after installation, correct the quickstart's Bash
  activation command, and clarify guided and prompt-free project creation.
  Update native function documentation for validation, mean handling, storage
  precision, and quantization behavior.

• Fix the missing quickstart pipeline diagram on the pkgdown website by
  referencing a vignette-local PNG that is copied into the rendered article.
  Installed vignette sources fall back to the existing package image.

• Correct reversed temporal-filter examples, zero-padded CompCor and motion
  column selections, AROMA mode support and its fMRIPrep removal version, and
  intensity-normalization variance scaling. Clarify ROI masking, censoring,
  minimum-voxel settings, local extraction, output-directory requirements, and
  connectivity limits. Refresh container setup, offline TemplateFlow guidance,
  debug-versus-dry-run behavior, scheduler polling defaults, article links,
  and contribution instructions; finish the intermediate-file documentation
  and make shell run-ID examples safe to copy after substituting the ID.

• Snapshot tracked worker scripts, helpers, and the BrainGnomes runtime into
  sealed, reusable project/run-owned bundles. Package reinstalls no longer
  change queued workers' startup code. Independent bootstrap handlers publish
  failure receipts and record non-array startup failures without loading
  BrainGnomes; external R dependencies and containers remain shared inputs.

• Register UUID submission attempts in SQLite before invoking Slurm, TORQUE,
  or local execution, including dynamically submitted postprocessing arrays.
  Workers can bind their own allocation IDs before submission returns, and
  late acknowledgements preserve started or completed states. Retain uncertain
  submissions, block duplicate launches of the same work unit and role, and
  expose these attempts through inspect_project()$submissions. Inspection
  and scheduler refresh remain read-only and SQLite-first.

• Aggregate Slurm array-task accounting under the tracked array identifier,
  preserving active and uncertain states until all observed tasks terminate.
  Distinguish scheduler query failures from missing records. Do not infer success
  from expired TORQUE records; verify retained completed jobs using exit status.
  Retain confirmed terminal observations while waiting for other jobs to finish.
  Scheduler refresh remains read-only and project summaries remain SQLite-first.

• Require tracked worker status updates to persist in SQLite or exit with an error.
  Store completion status, timestamp, and output manifest atomically so failed
  manifest writes cannot leave a falsely completed job in the tracking database.
  Close SQLite connections after rejected queries as well as successful ones.

• Extend spatial smoothing checks to isotropic and anisotropic voxel spacings
  of 1.8--4 mm and kernels 1.5--3 times geometric mean voxel spacing. Use smooth
  directional FWHM response functions only where calibration and independent
  validation meet the half-voxel error limit. Use operator replay for conditions
  whose FWHM response cannot meet that limit, preserving full-run SUSAN
  parameters and checking Gaussian output with the matching AFNI operator.
  Replay compares 96 distributed volumes in bounded chunks, rejects incorrect
  kernels and unchanged outputs, and records only compact QA metadata.
  Automatic checks also replay in-domain outputs whose FWHM comparison fails,
  retaining the failed comparison and the replay result separately in QA.
  The current continuous coefficient model passes for template-masked-input
  SUSAN; the other eight production contexts require replay.

• Calibrate SUSAN and Gaussian spatial validation for isotropic 2 mm images
  with 3--8 mm kernels using separate resolution-specific fits. Verify those
  fits on held-out subjects, including genuine 2 mm fMRIPrep outputs. Establish
  2 mm error limits from internal cohort-transfer checks, capped at 1 mm, while
  preserving coarser-resolution coefficients and limits. Reject unchanged
  images even when their predicted change is smaller than the error limit.

• Resample template masks and atlases using reference header geometry without
  loading the reference BOLD voxel data.

• Reject image objects, spatial arrays, and binary payloads before writing
  provenance JSON, configuration snapshots, validation records, or QC inventories.
  Keep image files out of provenance companion directories.

• Keep intensity-reference NIfTI voxel arrays out of derivative JSON; record
  published companion paths and compact header geometry instead. Validate
  intensity normalization across all volumes in bounded chunks to avoid
  memory spikes on long runs.

• Match QC validation audits to missing outputs through filesystem aliases,
  retaining their failed status instead of incorrectly marking them invalid.
  Canonicalize missing-configuration diagnostics consistently across platforms.
  Keep setup menu text portable and bound headless CLI tests so inherited
  Windows consoles cannot stall the test suite.

• Resolve relative configuration paths from a colocated project YAML: the YAML
  establishes the project root, all runtime and scheduler paths become
  absolute, and project-contained paths are saved portably relative to that
  root. Reject detached or mismatched project configurations before execution,
  and remove unsafe project_directory changes from the ordinary field editor.

• Ask about motion filtering after optionally adding framewise displacement
  during postprocessing setup, ensuring the saved stream records an explicit
  motion-filter decision and can be passed directly to run_project().

• Present temporal-filtering and intensity-normalization methods as descriptive
  numbered menus during guided setup instead of requiring users to type internal
  configuration values. Interactive prompts no longer insert an extra blank line
  between their final instruction and the input marker.

• Allow BrainGnomes setup_project (or init) with no project name to open the
  guided setup and prompt for the project name, project directory, and workflow
  settings. Supplying a project name retains prompt-free creation and defaults
  its project directory to the current working directory. Explicit project
  directories, configuration YAMLs, and saved run plans remain supported;
  overwriting a prompt-free configuration and retrying/cancelling work still
  require their existing explicit flags.

• Organize the website reference by task: setup, execution, monitoring and
  recovery, QC, provenance, and advanced tools.

• Remove diagnose_pipeline() and its export, without a compatibility wrapper.
  Use diagnose_project(); pass interactive = TRUE for the guided browser
  or interactive = FALSE for structured results. The CLI remains diagnose.

• Use the same selected-stage and stream configuration checks for plans, dry
  runs, and submission. Invalid licenses/resources now fail before project
  writes or scheduling, while unrelated stages/streams do not block selected
  work. Saved plans are revalidated at submission. Use steps (and optional
  stream selections) with validate_project_config() or config validate to
  inspect the same checks; exploratory invalid plans are explicitly labeled.

• Make CLI JSON output a single document on stdout, with progress, warnings,
  and log tails on stderr. Validate formats before acting, reject machine-format
  watch/interactive combinations, and require explicit stages for JSON runs.

• Make plans and dry runs concrete: show subject/session/stage/stream work,
  input/output and log locations, dependencies, per-job resources, and
  completion-marker skip decisions. Flywheel scope remains explicitly deferred.
  run_project(dry_run = TRUE) now returns a bg_project_plan instead of TRUE
  and no longer creates directories or repairs permissions. Full preview rows
  remain available in plan$preview$work and CLI JSON beyond the console limit.

• Resolve existing parent-directory aliases before rebasing missing template
  paths. Cloned projects now keep future Flywheel DICOM inputs and nested
  outputs under the new project on macOS, Windows, and symlinked filesystems,
  without creating those directories in the source project or shared inputs.

• Begin new guided setup with the user's starting point: DICOMs on Flywheel,
  local DICOMs, existing BIDS, or existing fMRIPrep derivatives. Preview the
  route, skip completed upstream stages, distinguish existing inputs from
  future download/output destinations, and retain explicit downstream choices.
  The menu also offers read-only project inspection and custom setup. Existing
  configured projects and targeted edits retain their selections; headless
  creation remains prompt-free. Use starting_point to preselect a guided route.

• Keep explicit run_project() arguments when choosing stages interactively,
  including dry_run = TRUE. The CLI preserves the same argument precedence.

• Retry exact failed subject/session/stage/stream combinations instead of
  recombining independent selections. Saved retry plans retain that scope and
  their source-run provenance; missing or ambiguous work fails safely.

• Isolate new projects created from templates: rebase project directories and
  give outputs, logs, scratch space, and tracking a fresh destination. Preserve
  external inputs and resource files, and inherit stage settings. Intentional
  sharing requires reuse_template_paths = TRUE (CLI: --reuse-template-paths).

• Restrict scheduler-contract checksums to recognized immutable execution
  inputs and explicitly selected environment artifacts. Mutable operational
  files, including SQLite tracking databases, logs, status markers, state
  files, receipts, and output manifests, remain recorded as environment
  metadata but no longer trigger false contract-drift failures when jobs start.

• Native postprocessing and ROI outputs now carry versioned JSON provenance,
  draft methods text, BibTeX, and available upstream citations and reports.
  Records distinguish executed, skipped, failed, and reused operations, retain
  actual confound columns and censor indices, and identify source files,
  atlas geometry, software, and applicable run/job records. Use
  read_derivative_provenance() to inspect a derivative without SQLite and
  export_derivative_provenance() to copy it with verified companions into a
  portable bundle. Generated methods always require human review. Existing
  derivatives without producer records are explicitly marked unknown.

• Add collect_qc_inventory(), write_qc_inventory(), and
  render_qc_dashboard() for study QC snapshots. R objects and TSV tables join
  configured workflow expectations, job history, derivative availability,
  postprocessing audits, original fMRIPrep motion summaries, MRIQC IQMs, censor
  masks, and regional voxel retention. The optional Quarto dashboard includes
  searchable React tables, interactive plots, expandable evidence, and snapshot
  downloads. Collection is read-only; no human review or inclusion decisions
  are implemented.

• Treat platform-equivalent filesystem spellings as one QC path identity,
  preventing duplicate derivative rows from Windows short/long path aliases.

• Consolidate project creation in setup_project(). It now supports portable,
  prompt-free creation with interactive = FALSE, including templates and
  overwrite control. The headless BrainGnomes init command uses this pathway,
  and the redundant initialize_project() entry point has been removed.

• Remove the redundant doctor() R alias before 1.0. Use
  doctor_project() for R preflight checks; the BrainGnomes doctor CLI
  command remains available.

• Harmonize project inputs across the R lifecycle API. load_project(),
  edit_project(), validate_project_config(), doctor_project(),
  plan_project(), run_project(), run_bids_validation(), status and log
  helpers, provenance inspection, retry, and cancellation now default to the
  current working directory and accept project configuration objects, YAML
  files, or project directories where applicable.

• Distinguish optional request plans from final scheduler contracts. Plans now
  report whether their subject scope is resolved or deferred. Flywheel runs
  record the realized post-sync scope before downstream submission; every
  tracked scheduler job receives an immutable pre-submission manifest and a
  compute-host runtime receipt that verifies execution-driving files. Structured
  work-unit and contract fields are stored in the tracking database with an
  automatic migration for existing projects.