v0.5.0-beta25

Lungfish 0.5.0-beta25

Previous release: v0.5.0-beta24

This is a focused usability update for choosing reference sequences. The reference
menu in FASTQ/FASTA Operations had started showing the complete path to each bundle's
internal sequence payload, such as
Downloads/NC_078297.lungfishref/genome/sequence.fa.gz. That path was technically
precise but made the menu unnecessarily wide and forced the meaningful part, the
reference bundle's name, to compete with storage details.

Reference pickers show bundle names again

Reference choices now lead with the bundle's human-readable name. A unique reference
appears simply as a name such as Dar_es_Salaam or NC_078297, without exposing the
internal genome/sequence.fa.gz path in the menu. This applies to minimap2 and to the
other read mappers that share its configuration sheet, including BWA-MEM2, Bowtie2,
and BBMap. Viral Recon's local-reference menu and the reusable reference picker used
by orientation, PBAA, ONT genotyping, and haplotype-definition workflows receive the
same correction.

Folder context appears only when it carries information. If two references have the
same visible name in different parts of a project, Lungfish adds their containing
folders, for example NC_078297 (Downloads) and
NC_078297 (Analyses/minimap2-2026-08-09). In the rare case that matching names also
share a folder, the menu falls back to the source bundle or FASTA path so every choice
remains distinct. References whose names are already unique stay uncluttered.

The exact FASTA payload has not changed. Mapping configuration still retains and shows
the selected sequence path in its detail text, and every picker continues to identify
the same underlying reference URL. This update changes presentation only; it does not
modify scientific inputs, outputs, bundle contents, mapping parameters, or provenance.

Stability and release maintenance

The shared label resolver is covered by regression tests for unique bundles,
same-named bundles in separate locations, standalone FASTA files, same-folder
collisions, and names that resemble a folder-qualified label. The mapping dialog and
shared picker targets are also compiled and exercised with the existing focused test
suites so the corrected labels reach each tool without changing selection behavior.

The app, embedded command-line tool, Help Book, and managed-tool metadata report
0.5.0-beta25. This remains a beta prerelease distributed through a signed and
notarized Apple Silicon DMG. Sparkle beta and legacy alpha-bridge users receive this
narrative as the update notification for the new build.