BioOKF v0.3.1

BioOKF 0.3.1 repairs Studio's in-app updater. On 0.3.0, accepting an update quit
Studio and then never brought it back: nothing was installed, and the app did not
reopen. This release fixes that, and is packaged so that Macs already running the
broken 0.3.0 updater can still install it and recover on their own.

The Bug

Studio picks the first release asset matching the running platform, and the
GitHub API does not return assets in upload order. It therefore chose
biookf-macos-<arch>.tar.gz — built in CI with --no-sign — rather than the
signed DMG. The updater's relauncher then ran codesign --verify under
set -euo pipefail, which aborted the script. Because Studio had already quit
before any of this was checked, the app simply vanished, and the only trace was a
line in ~/Library/Logs/BioOKF Studio Updater.log.

Fixes

• The updater now prefers the signed .dmg over any tarball, instead of taking
  whichever asset GitHub listed first.
• The download is unpacked and signature-checked before Studio quits. A bad
  asset now surfaces as an error in the update dialog with Studio still running.
• An update must be signed by the same Developer ID team as the running app.
• Replacing the app is atomic: the new bundle is copied in and verified before
  the old one is moved aside, and any failure restores it. The previous installer
  ran rm -rf on the installed app before copying the replacement.
• The relauncher reopens Studio on every exit path, including failures.
• Dropped the spctl --assess gate, whose result depended on whether the user
  had Gatekeeper assessments enabled rather than on the download.
• The privileged install step no longer depends on an inherited PATH, so
  ownership of the installed bundle is restored instead of being left as root.

Packaging

• Both macOS assets — the DMGs and the biookf-<target>.tar.gz archives the
  plugin installs from — are now signed, notarized, and stapled.
• .github/workflows/release.yml no longer publishes release assets. Its runners
  hold no Developer ID certificate, so anything they build is unsigned and cannot
  be installed by the updater. It now runs as a tag-time verification build.

For Studio Users

• Download BioOKF.Studio_0.3.1_aarch64.dmg for Apple Silicon Macs.
• Download BioOKF.Studio_0.3.1_x64.dmg for Intel Macs.
• If you are on 0.3.0, the in-app update should now work. If Studio previously
  quit on you during an update, it was never uninstalled — reopen it from
  /Applications.

Verification Targets

• Rust tests for biookf-studio, bokf-cli, and bokf-mcp.
• Updater tests covering asset ranking, signature and team-identity gating,
  atomic install with rollback, relaunch on every failure path, and the
  bash/AppleScript/shell quoting of the privileged install command.
• The v0.3.0 relauncher replayed against both the old unsigned tarball (fails, as
  users experienced) and the new signed tarball (installs and relaunches).
• Signed, notarized, and stapled Apple Silicon and Intel DMGs and tarballs,
  each re-verified after a tar round-trip.

BioOKF 0.3.0

BioOKF Release Notes

v0.3.0 - 2026-07-02

BioOKF 0.3.0 is a Studio-focused release. It keeps the CLI, MCP server, and
Tauri desktop app on the same engine, and adds a shareable graph export path for
people who need to review or circulate a knowledge base outside the desktop app.

Highlights

• Added a Studio graph export button below the zoom and fit controls.
• Exported graphs are self-contained HTML files with embedded data, styling, and
  interaction code. They open directly in a browser without a local server.
• Exported HTML graph views support pan, zoom, search, clickable nodes and
  edges, and a responsive detail drawer for fields, provenance, notes, outgoing
  edges, incoming edges, and rendered document text.
• Polished the Studio canvas control stack so zoom in, zoom out, fit-to-view,
  and export read as a cohesive minimal set.
• Updated release metadata, plugin manifests, marketplace metadata, installer
  documentation, and the public landing page for the 0.3.0 release.

For Studio Users

• Download BioOKF.Studio_0.3.0_aarch64.dmg for Apple Silicon Macs.
• Download BioOKF.Studio_0.3.0_x64.dmg for Intel Macs.
• Use the export control in the lower-right graph toolbar to save the active
  graph as a portable HTML file.

For Agent And Plugin Users

• The bundled Claude Code and Codex plugin metadata now points at v0.3.0.
• The plugin launcher default BIOOKF_VERSION is now v0.3.0, while still
  allowing overrides through the environment.
• Existing MCP tool names and CLI commands remain compatible with 0.2.x.

Verification Targets

• Rust tests for biookf-studio, bokf-cli, and bokf-mcp.
• Studio HTML export browser checks across desktop and mobile viewports.
• Signed and notarized Apple Silicon and Intel Studio DMGs.
• GitHub Release assets for macOS CLI/MCP archives and Studio DMGs.

DMG Checksums

56ce2fa313784bf06c36e8d72f89983f30312a08e82fbe5b3ce1af8f0f066d72  BioOKF.Studio_0.3.0_aarch64.dmg
b2f59c17ab2e98fc795fd26936e9b333b4bdae6ec11fc7b3be0cf7aa24c03951  BioOKF.Studio_0.3.0_x64.dmg

Archive Checksums

71b55d02e2c229568ec0cb300ef2479c05e0d84172353b01bdbdd0757c79388f  biookf-macos-arm64.tar.gz
b25b0be67266143269e47fe597bce8815a2305e17ecc8f26926088325c92cca5  biookf-macos-x64.tar.gz

Local Artifact Verification

• Apple notarization accepted for both Apple Silicon and Intel app bundles.
• Outer DMG notarization accepted, stapled, and validated for both DMGs.
• Mounted DMG app bundles passed codesign --verify --deep --strict.
• Embedded bokf and bokf-mcp binaries passed strict codesign verification.
• Mounted Apple Silicon bokf reports bokf 0.3.0.

Remote Workflow Verification

• GitHub Actions release run 28631702487 completed successfully for macos-arm64 and macos-x64.
• The release contains signed/notarized Studio DMGs and unsigned convenience app archives for both macOS architectures.

BioOKF 0.2.3

BioOKF 0.2.3 refreshes the Studio graph renderer and republishes notarized macOS installers for both Apple Silicon and Intel.

Highlights:

• Adds hub-aware dense graph layout so high-degree central nodes get more breathing room and peripheral neighborhoods organize around them.
• Makes node size meaningful with nonlinear degree/centrality scaling and a capped maximum size.
• Keeps graph physics responsive after drag/drop with collision cleanup and repulsion reheating, so dragged nodes do not remain stacked on neighbors.
• Restores the top-panel warning/error count indicator and tightens the graph control icon sizing.
• Fixes large EBVMS-style bundle loading by rendering a graph-first payload, skipping raw media/PDF hydration, and lazy-loading node details.
• Widens zoom range and adds density-aware edge/node-border fading so dense zoomed-out views read lighter while close-up views keep normal contrast.

Assets:

• BioOKF.Studio_0.2.3_aarch64.dmg - Apple Silicon notarized/stapled installer
  • SHA-256: c957c5251c869ae4237b7581ab2634c8b7ef0d4d28ef101f00669f107a8b4374
• BioOKF.Studio_0.2.3_x64.dmg - Intel notarized/stapled installer
  • SHA-256: 95ed7b4e804adc33b5ee2c7f6ebf77beac86c8405b4622e90b111e991124458d
• biookf-macos-arm64.tar.gz - plugin fallback bundle with signed CLI/MCP plus Studio.app
  • SHA-256: 67e5047d84120c3bca3127926f47d02d2c42e0a87f26352dab1c9cb90736abff
• biookf-macos-x64.tar.gz - plugin fallback bundle with signed CLI/MCP plus Studio.app
  • SHA-256: c5e0db9254bb5d12320ce7d6ffdc83e351835709b2ebdee5ce75cce85ea2f2d7

Validation coverage:

• Apple notarization accepted for both app bundles and both downloadable DMGs; both DMGs were stapled and xcrun stapler validate passed.
• Mounted both DMGs and verified BioOKF Studio.app with codesign --verify --deep --strict and spctl --assess --type execute; both reported Notarized Developer ID.
• Verified bundled bokf and bokf-mcp signatures inside each mounted app, with arm64 binaries in the Apple Silicon DMG and x86_64 binaries in the Intel DMG.
• Ran cargo test -p bokf-core, cargo test -p biookf-studio, and node --check app/studio/dist/app.js during the Studio renderer fix pass.
• Smoke-tested EBVMS graph loading at 1,793 nodes / 6,901 edges with zero layout overlaps, and checked BioRED zoom/density behavior across wide zoom levels.

BioOKF v0.2.2

BioOKF Studio 0.2.2 release: notarized macOS Studio DMG, Codex plugin manifest, MCP ingestion hardening, and graph performance fixes.

BioOKF v0.2.1

Full Changelog: v0.2.0...v0.2.1

BioOKF v0.2.0

Full Changelog: v0.1.0...v0.2.0

BioOKF v0.1.0

First release of the BioOKF toolchain as an installable Claude Code plugin — the bokf CLI, the bokf-mcp server, and the BioOKF Studio desktop app, prebuilt.

Install (Claude Code)

/plugin marketplace add Broccolito/BioOKF
/plugin install biookf@biookf

Restart Claude Code. The first tool call downloads the prebuilt bundle for your platform — no compiling.

Assets

Each biookf-<platform>.(tar.gz|zip) contains bin/bokf, bin/bokf-mcp, and the BioOKF Studio app.
biookf-macos-arm64.tar.gz is attached here; macOS-x64, Linux, and Windows builds are produced by the release CI and attach shortly after tagging.

See the README for the full tool reference.

Full Changelog: https://github.com/Broccolito/BioOKF/commits/v0.1.0

Full Changelog: https://github.com/Broccolito/BioOKF/commits/v0.1.0

Full Changelog: https://github.com/Broccolito/BioOKF/commits/v0.1.0

Full Changelog: https://github.com/Broccolito/BioOKF/commits/v0.1.0