                 Changes in version 0.99.3 (2026-07-22)                 

  - NAMESPACE: use selective @importFrom only (no wholesale
    import(shiny), import(DT), or import(jsonlite)) so loading no longer
    warns about replacing renderDataTable, dataTableOutput, or validate.
  - .Rbuildignore: exclude duplicate R/shiny_* / R/ui_* helpers; the app
    runs from inst/shinyapp/ and attaches only shiny + bslib at launch.
  - Align app/engine version strings (APP_VERSION, ACMG_PRO_ENGINE) with
    package DESCRIPTION version 0.99.3.
  - Vignettes: Bioconductor vs GitHub install/reinstall paths and app
    step summary.
  - Check NOTES: ignore LICENSE.md; ship only ClinicalVariantR*.Rmd
    vignettes.
  - Remove unused crosstalk dependency; keep dependency bootstrap only
    under scripts/ (not shipped in the Bioconductor tarball).
  - Fix package Rd wording that broke PDF manual generation; keep
    DESCRIPTION free of blank lines between fields.
  - BiocCheck: drop inst/CITATION until a preprint/publication DOI
    exists; expand Description to three sentences; avoid paste in a
    condition message.

                 Changes in version 0.99.2 (2026-07-20)                 

  - Fix analysis crash on variants with pathogenic VEP CLIN_SIG in CSQ:
    rbind failed when merging ClinVar protein DB (extra source column)
    with the CSQ catalog (numbers of columns of arguments do not match).
  - R CMD check: .Rbuildignore now uses ^data/ (and similar) so
    development non-R assets under data/ are excluded; package samples
    remain in inst/extdata/. Roxygen @importFrom tags keep NAMESPACE
    Imports wired.

                 Changes in version 0.99.1 (2026-07-17)                 

  - R CMD check / R-universe WARNING cleanup:
      - Ship non-R assets under inst/extdata/ (and ignore package-root
        data/).
      - ASCII-only package R/ sources (em/en dashes and similar
        replaced).
      - Declare digest / openssl Imports used by auth storage.
      - Wire NAMESPACE imports for bslib, VariantAnnotation, and
        methods.
      - Declare optional shinyjs in Suggests (Group B run-button
        enable/disable).
      - Add .Rbuildignore for development-only root Shiny/config/scripts
        trees.

                 Changes in version 0.99.0 (2026-07-08)                 

  - Initial Bioconductor submission scaffold (x.99.y versioning).
  - Interactive Shiny platform for ACMG/AMP germline variant
    classification from VEP / SnpEff / ANNOVAR-annotated VCFs.
  - Three workflows: full clinical (Group A), automated rapid (Group B),
    and gene-panel (Group C).
  - Streaming whole-VCF analysis with optional bcftools acceleration.
  - Structured criterion-level evidence export and reproducibility
    metadata.
  - Package entry points: ClinicalVariantR() / ClinicalVariantRApp()
    return a Shiny app object (user launches with shiny::runApp()).
  - Vignettes: introduction and run/test guide covering app launch,
    sample data, UI checks, and CLI/unit tests.
