Changes in version 1.1.0                        

  - Detect native symbolic links, dangling links and Windows junctions
    without relying on the Windows Sys.readlink() stub; retain manifest
    and overwrite boundaries across platforms.

  - Preserve unavailable marker measurements through correction and
    state calling; honor configured methods/support and validate ordered
    source and score bindings.

  - Correct mixture overlap diagnostics and isolate cells by image and
    cell ID.

  - Replay identity/state cuts, enablement and undo through the shared
    classifier. Validate checkpoint contents and detect stale concurrent
    sessions.

  - Add real review controls, checkpoint/resume, explicit human review
    status and verified snapshot download. Render plots correctly and
    summarize dotplot means.

  - Introduce version 2 snapshots/checkpoints and unambiguous data
    hashes. Bind all replay inputs, outputs, review decisions and
    status; reject mutated snapshots and verify staged exports before
    publication. Preserve exact decimal scores.

  - Legacy records are preserved; regenerate/review into new paths.
    Explicit unverified inspection remains available for legacy exports.
    Frozen residual parameters require explicit import and downstream
    requalification, not refitting.

  - Fix every plot helper (gk_plot_density(), gk_plot_thresholds(),
    gk_plot_map(), gk_plot_dotplot(), gk_plot_states(),
    gk_plot_embedding() and gk_plot_overview()), which failed when drawn
    with "Can't subset .data outside of a data mask context". The tests
    now build each plot instead of only checking its class.

  - Standardize the named v5 package logo across README, documentation
    pages and available application headers, with matching light and
    dark artwork.

  - Add fixed numerical threshold calls and state diagnostics with
    explicit parent eligibility, localization, missingness and
    non-authorizing audit outputs.

  - Add authenticated external residual-parameter import without
    fitting, fixed raw-support-aware ternary calls, and declarative
    candidate rules with explicit unavailable states. These APIs never
    authorize scientific review or production.

  - Preserve review session ownership across checkpoint saves, reject
    foreign-owner writes, and serialize save/load operations with a
    separate filesystem lock.

  - Added gk_fit_residual_model() and gk_apply_residual_model() for
    freezing common-score identity and first-principal-component panel
    residual spaces. Application reuses fitted parameters without
    refitting, requires the exact marker dictionary, and preserves
    optional missing values. Content hashes bind model parameters, typed
    metadata and caller-supplied threshold records. Raw-channel support,
    training-image scope and biological decisions remain explicit caller
    responsibilities; existing gk_correct() behavior is unchanged.

  - Cell-table readers recognize canonical cellspecR directories in
    Parquet and typed TSV formats. Explicit canonical writes delegate to
    cellspecR and preserve metadata, adjacency and exact numeric values.
    They require the optional cellspecR dependency and valid declared
    image calibration.

  - gk_write_cellspec() retains its legacy default for compatibility and
    adds an explicit format argument. The legacy format is planned for
    retirement after migration is qualified; new integrations should
    select canonical "parquet" or "tsv.gz". Schema errors never trigger
    a legacy fallback.

                        Changes in version 1.0.0                        

Initial package implementation; CRAN publication was not established.

  - Added the study-neutral configuration model, cellspec 1.0 adapter,
    preparation and callability checks, simulator, and bundled example
    data.
  - Added reproducible score corrections, per-image threshold estimation
    with evidence, and PCA/UMAP population embeddings.
  - Added declarative classification, state calls, structure review,
    append-only review ledgers, persistence, immutable snapshots, and
    verifiable exports.
  - Added plotting helpers, a Shiny review shell, reproducibility
    vignettes, and benchmark templates.