Biorouter v1.88.5

Biorouter v1.88.5 release notes

Release date: July 21, 2026

Repository: github.com/BaranziniLab/biorouter

Biorouter v1.88.5 is an agent-autonomy and desktop-polish release. It introduces
Fully-Automatic mode — the agent works with broad file autonomy and only stops
to ask about genuinely sensitive system operations — hardens the permission engine
against a class of false-positive prompts that could stall an unattended run, and
lands a round of desktop chat, tab, terminal, and artifact-preview fixes on top of
the v1.88.3 interface-cohesion work.

Existing settings, sessions, providers, extensions, skills, workflows,
applications, knowledge bases, and usage history remain compatible.

Downloads

Platform	File	Install
macOS Apple Silicon	Biorouter-1.88.5-arm64.dmg	Open the DMG and drag Biorouter.app to /Applications
macOS Intel	Biorouter-1.88.5-x64.dmg	Open the DMG and drag Biorouter.app to /Applications
Windows x64	Biorouter-win32-x64-1.88.5.zip	Unzip and run Biorouter.exe
Linux desktop Debian / Ubuntu	biorouter_1.88.5_amd64.deb	sudo apt install ./biorouter_1.88.5_amd64.deb
Linux desktop Fedora / RHEL	Biorouter-1.88.5-1.x86_64.rpm	sudo dnf install ./Biorouter-1.88.5-1.x86_64.rpm
Linux CLI + daemon Debian / Ubuntu	biorouter-cli_1.88.5_amd64.deb	sudo apt install ./biorouter-cli_1.88.5_amd64.deb
Linux CLI + daemon Fedora / RHEL	biorouter-cli-1.88.5-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.88.5-1.x86_64.rpm

The macOS builds are signed with the UCSF Developer ID, notarized by Apple, and
stapled. Signed updater ZIPs for both Mac architectures and latest-mac.yml are
included for one-click in-app updates. The CLI + daemon packages install the
headless biorouterd server and the interactive biorouter terminal client
without the desktop GUI.

Fully-Automatic mode

• A new Fully-Automatic permission mode gives the agent broad autonomy over
  ordinary file work — reading, writing, and editing inside your project run
  without a prompt — while still stopping to ask before a small, well-defined set
  of sensitive system operations (writes or deletes under system directories,
  SSH keys, keychains, launchd/login items, and browser credential stores).
• The mode is the recommended default for long, unattended agent runs: it keeps
  the loop moving without a permission prompt on every edit, but preserves a hard
  approval floor around the operations that actually carry blast radius.

Permission-engine hardening

The sensitive-operation classifier that backs Fully-Automatic mode was tightened
so it stops on real risk and stays out of the way otherwise:

• /dev/null and the benign character devices are no longer flagged. A routine
  … 2>/dev/null redirect — or a /dev/null literal embedded in code the agent
  writes — used to be misread as a write to a "protected system directory" and
  raise a Destructive approval prompt that Fully-Automatic mode never
  auto-approves, silently stalling autonomous agents. Writes to /dev/null,
  /dev/std{in,out,err}, /dev/tty, /dev/zero, and /dev/fd/* are now treated
  as ordinary; real writes to /etc, ~/.ssh, and block devices are still gated.
• Sensitive writes hidden inside shell command lines and execute_code bodies
  are detected (redirect targets and mutating-binary arguments), while
  angle-bracket prose placeholders like <word> are no longer misread as shell
  redirects.
• The text_editor working-directory jail is relaxed in Auto mode so ordinary
  project edits are not blocked, without loosening the catastrophic-path denylist.

Desktop chat, tabs, and terminals

• Window focus and per-pane terminals. The "Always on Top" toggle no longer
  silently pins the first window (it was bound to a stray accelerator), and its
  menu state tracks the focused window. In-app terminals are scoped to their own
  chat pane rather than spanning the whole window, and each opens in that
  session's working folder.
• Grabbable split dividers. Dividers between split chat panes can now be
  dragged to resize — they were painted under the chat content and swallowed the
  pointer. Both row and column dividers drag smoothly and preserve their ratio on
  window resize.
• Split cap raised from 4 to 6 panes.
• Composer toolbar collapse. When the composer row gets too narrow the tool
  pickers collapse behind a lower-left + popover instead of overlapping, then
  expand again when there is room.
• Chat names stay in sync across Recents, history, tabs, and diverged
  branches — the backend-owned canonical name now propagates everywhere, including
  the locked (branch N) diverge names.
• Drag-to-reorder tabs track the pointer instead of jumping away from it.

Artifact preview

• Files an agent creates inside code_execution now surface in the artifact
  side panel, not just files written by a top-level editor call.
• The markdown preview renders images and links correctly.
• The folder preview no longer occasionally opens the wrong directory —
  same-basename folders are disambiguated and unanchorable relative paths are
  dropped rather than resolved against the wrong root.
• Auto-open of a new artifact is a tested pure decision, and the historical-reload
  guard is locked so reopening an old session does not silently resume it.

Chat reliability

• A rapid double-submit no longer appends a phantom duplicate user bubble, and
  a transient send/load backend blip degrades to an inline retryable error
  instead of the fatal session card.
• Soft interrupt and hard stop are acknowledged immediately, and a user's own
  submit always returns them to the bottom of the conversation.
• Terminal PTY slots are no longer leaked on reload, and a stale resumeSessionId
  is cleared from the URL when an empty New Session tab takes focus.

Themes and observability

• Theme families are generated from one definition file per family; the Alma
  Mater family is recoloured to UCSF teal and a JupyterLab-inspired Roche Limit
  family is added.
• Structured per-tool-result logging gives every tool call a machine-readable
  record for observability and debugging.

Documentation

• The documentation tree was reorganized and brought to a single house style
  in a per-folder audit, a dev-GUI launch guide was added for driving the app from
  a shell without a TTY, and a docs conformance linter guards the format.

Release verification

The 1.88.5 release pipeline verifies Rust formatting, strict linting, workspace
tests, generated API consistency, desktop type-checking and tests, signed and
notarized macOS arm64/x64 apps, the Windows desktop package, Linux DEB/RPM desktop
packages, and the CLI + daemon Linux packages. The full Rust library suite
(1493 tests) and the desktop unit suite pass, and the built app was smoke-tested
end-to-end (UI and agent loop) before publication.

Biorouter v1.88.3

Biorouter v1.88.3 Release Notes

Release date: July 18, 2026

Repository: github.com/BaranziniLab/biorouter

Biorouter v1.88.3 completes the interface-cohesion redesign and relicenses the
brand mark. The BioRouter wordmark and BR icon are now set in Inter (an
open-licensed typeface that may legally be used as a logo), the desktop chat and
sidebar gain a cohesive tab, terminal, and navigation model, and a round of
artifact-preview and permission hardening carries over from the interim work.

Existing settings, sessions, providers, extensions, skills, workflows,
applications, knowledge bases, and usage history remain compatible.

Downloads

Platform	File	Install
macOS Apple Silicon	Biorouter-1.88.3-arm64.dmg	Open the DMG and drag Biorouter.app to /Applications
macOS Intel	Biorouter-1.88.3-x64.dmg	Open the DMG and drag Biorouter.app to /Applications
Windows x64	Biorouter-win32-x64-1.88.3.zip	Unzip and run Biorouter.exe
Linux desktop Debian / Ubuntu	biorouter_1.88.3_amd64.deb	sudo apt install ./biorouter_1.88.3_amd64.deb
Linux desktop Fedora / RHEL	Biorouter-1.88.3-1.x86_64.rpm	sudo dnf install ./Biorouter-1.88.3-1.x86_64.rpm
Linux CLI + daemon Debian / Ubuntu	biorouter-cli_1.88.3_amd64.deb	sudo apt install ./biorouter-cli_1.88.3_amd64.deb
Linux CLI + daemon Fedora / RHEL	biorouter-cli-1.88.3-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.88.3-1.x86_64.rpm

The macOS builds are signed with the UCSF Developer ID, notarized by Apple, and
stapled. Signed updater ZIPs for both Mac architectures and latest-mac.yml are
included for one-click in-app updates. The CLI + daemon packages install the
headless biorouterd server and the interactive biorouter terminal client
(full-screen TUI) without the desktop GUI.

New brand identity — the mark is now Inter

• The BioRouter wordmark ("Bio" in UCSF navy, "Router" in coral, over a short
  split underline) and the BR app icon are set in Inter (SIL Open Font
  License). The previous native-system rendering resolved to SF Pro, which Apple
  licenses for interface text but not for use as a logo; Inter is licensed for
  exactly this purpose and renders identically on every platform.
• Every shipped surface is regenerated from one source: the dock/taskbar app
  icon (ICNS/ICO/PNG), the macOS menu-bar template, the in-app sidebar lockup,
  the CLI logos, and the landing site.
• The app icon is inset to the macOS icon safe-area so it no longer reads
  oversized next to native applications in the Dock.

Cohesive desktop chat, tabs, and terminal

• Tabs collapse into an overflow menu when the strip runs out of room, and
  chat groups can be merged into one strip or split back apart. A "+" control
  opens a new chat tab to the right of the last tab, and dragging a tab out now
  tracks the pointer instead of jumping away from it.
• The in-app terminal is scoped to the individual chat tab (not shared across
  the whole window) and opens in that session's working folder. Cmd/Ctrl+T is
  focus-aware — a new terminal tab when the terminal is focused, a new chat tab
  otherwise — and its "+" is left-aligned to match the chat tabs.
• The sidebar flies the new wordmark, aligns its divider and Recents well to
  the navigation labels, and shows the count of chats from the past seven
  days (with an explanatory tooltip) rather than a meaningless buffer count.
• The default window is larger so the usage heatmap and Recents are both visible,
  and the Home view folds Recents before the heatmap as the window shrinks.

Artifact preview and reliability

• The artifact side panel previews Jupyter notebooks (markdown, code, stream,
  DataFrame, image, and error cells) and shares the same status strip as the rest
  of the preview surfaces.
• The extension-loading toast counts only the user's own extensions — bundled
  built-in servers, which always load, are excluded from the "x of y" tally.
• Renderer-to-main navigation and MCP-UI prompt actions are guarded by the local
  file-permission policy and scoped to the chat they originate from, with focused
  regression tests. A brand-mark render loop that could blank the app on mount was
  fixed (measure once on mount and on font load, not every render).

Release verification

The 1.88.3 release pipeline verifies Rust formatting, strict linting, workspace
tests, generated API consistency, desktop type-checking and tests, signed and
notarized macOS arm64/x64 apps, the Windows desktop package, Linux DEB/RPM
desktop packages, and the CLI + daemon Linux packages.

BioRouter v1.88.1

BioRouter v1.88.1 Release Notes

Release date: July 15, 2026

Repository: github.com/BaranziniLab/biorouter

BioRouter v1.88.1 is a focused reliability and control release. It adds a
selective factory-reset surface, makes the Home activity view appear
immediately from bounded caches, hardens bundled local-model startup and
warm-up, fixes theme-pack persistence, and normalizes tooltip layout across the
desktop and generated visualizations. The production desktop dependency graph
also moves to patched, semver-compatible releases and passes its production
security audit with no known vulnerabilities.

There are no required migrations. Existing settings, sessions, extensions,
skills, workflows, applications, knowledge bases, and usage history remain
untouched unless the user explicitly selects them in the new reset panel.

Downloads

Platform	File	Install
macOS Apple Silicon	BioRouter-1.88.1-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS Intel	BioRouter-1.88.1-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows x64	BioRouter-win32-x64-1.88.1.zip	Unzip and run BioRouter.exe
Linux desktop Debian / Ubuntu	biorouter_1.88.1_amd64.deb	sudo apt install ./biorouter_1.88.1_amd64.deb
Linux desktop Fedora / RHEL	BioRouter-1.88.1-1.x86_64.rpm	sudo dnf install ./BioRouter-1.88.1-1.x86_64.rpm
Linux CLI only Debian / Ubuntu	biorouter-cli_1.88.1_amd64.deb	sudo apt install ./biorouter-cli_1.88.1_amd64.deb
Linux CLI only Fedora / RHEL	biorouter-cli-1.88.1-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.88.1-1.x86_64.rpm
Headless Linux x64	biorouter-headless-linux-x64.tar.gz	Extract and follow docs/headless-linux.md

The macOS builds are signed, notarized, and stapled with the UCSF Developer ID.
Signed updater ZIPs for both architectures and latest-mac.yml are included for
in-app updates.

Highlights

Selective reset controls

Settings → App now includes a reset panel that previews affected item counts
before any deletion and requires explicit confirmation. Users can reset one or
more independent categories:

• Agent Drafter applications;
• knowledge bases and Soul memory;
• user-installed skills;
• custom extensions while retaining bundled capabilities;
• schedules while restoring Daily Meditation;
• workflows while restoring the Meditation workflow; and
• conversation, usage, cost, and checkpoint history.

Resetting everything uses the same category-specific operations rather than an
opaque directory wipe. Active agent turns block the operation, cached agents
and renderer caches are cleared safely, built-in content is restored, and the
desktop refreshes affected usage and navigation state after completion.

Immediate Home activity

• Home activity and recent sessions use short-lived, bounded caches so the
  dashboard can paint useful data immediately and reconcile in the background.
• Hovering or focusing Home in the sidebar preloads both activity and recent
  session data.
• The activity heatmap identifies cells in the current streak in its accessible
  label, tooltip, and legend.
• Failed refreshes preserve usable cached data instead of replacing it with an
  empty surface.

More dependable local models

• Bundled llama.cpp startup detects and terminates stale listeners before
  retrying, reducing false “address already in use” failures after an
  interrupted launch.
• The LLAMACPP_ENABLE_THINKING setting accepts both typed booleans and string
  environment values.
• Warm-up requests allow thinking-capable models enough output budget to reach
  their readiness response.
• Gemma 4 E2B download-size guidance now reflects the curated artifact.
• Repetition-loop signatures canonicalize nested JSON object keys, keeping
  equivalent tool calls equivalent in both standalone and full-server builds.

Desktop polish and theme reliability

• Imported theme packs retain their selected values and present consistently
  after restart.
• Built-in, model, network, and generated-visualization tooltips share bounded
  wrapping and viewport-aware placement.
• Short labels stay on one line where space permits; long diagnostic content
  wraps without escaping its canvas.
• The original BioRouter identity and platform icons remain unchanged in this
  release.

Production dependency hardening

• Patched releases of the desktop routing, request-throttling, URL parsing,
  shell quoting, and utility dependencies replace their vulnerable revisions.
• npm audit --omit=dev reports zero vulnerabilities for the dependency graph
  shipped inside the desktop and headless packages.
• The complete 886-test desktop suite passes against the refreshed lockfile.

Documentation

• The design, theme, and agentic-system references now document the current
  desktop tokens, theme contract, runtime loop, session boundaries, tools,
  permissions, checkpoints, interrupts, vault binding, and completion gates.
• The landing documentation and download matrix cover every v1.88.1 desktop,
  CLI-only, and headless artifact.

CLI, TUI, server, and headless parity

The biorouter CLI and terminal UI, biorouterd daemon, desktop-bundled
binaries, Linux CLI packages, and headless browser/server archive all report
1.88.1. The CLI/TUI continues to expose terminal chat, provider and model
selection, workflows, scheduling, knowledge, extensions, skills, diagnostics,
web mode, and biorouter doctor without requiring Electron.

Release verification

Publication is gated on the repository release pipeline:

• Rust formatting, linting, workspace tests, generated API consistency, and the
  complete desktop test suite;
• signed, notarized, and stapled Apple Silicon and Intel applications, mounted
  from their DMGs and launched with packaged biorouter and biorouterd;
• Linux desktop DEB and RPM installation and startup in clean containers;
• CLI-only DEB and RPM installation plus terminal entry-point and version
  checks;
• headless archive integrity, daemon health, browser startup, and HTTP fetch;
• Windows CLI, daemon, terminal entry point, and desktop startup on a native
  Windows GitHub-hosted runner; and
• artifact architecture, updater-manifest, checksum, and release-name checks.

Upgrade notes

No configuration changes are required. macOS users on v1.86.0 or later can use
the in-app Restart & Update action. Everyone else can install the package for
their platform over the current version.

BioRouter v1.88.0

BioRouter v1.88.0 Release Notes

Release date: July 14, 2026

Repository: github.com/BaranziniLab/BioRouter

BioRouter v1.88.0 is a broad reliability, safety, performance, and interface
release across the desktop app, terminal UI, agent runtime, Agent Drafter,
headless server, and cross-platform distribution pipeline. It makes long-running
agent work more controllable, reports usage more honestly, brings generated
artifacts directly into chat, and gives every supported window size a complete,
calmer workspace.

There are no required configuration migrations. Existing settings, sessions,
extensions, skills, workflows, knowledge bases, and usage history are preserved.

Downloads

Platform	File	Install
macOS Apple Silicon	BioRouter-1.88.0-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS Intel	BioRouter-1.88.0-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows x64	BioRouter-win32-x64-1.88.0.zip	Unzip and run BioRouter.exe
Linux desktop Debian / Ubuntu	biorouter_1.88.0_amd64.deb	sudo apt install ./biorouter_1.88.0_amd64.deb
Linux desktop Fedora / RHEL	BioRouter-1.88.0-1.x86_64.rpm	sudo dnf install ./BioRouter-1.88.0-1.x86_64.rpm
Linux CLI only Debian / Ubuntu	biorouter-cli_1.88.0_amd64.deb	sudo apt install ./biorouter-cli_1.88.0_amd64.deb
Linux CLI only Fedora / RHEL	biorouter-cli-1.88.0-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.88.0-1.x86_64.rpm
Headless Linux x64	biorouter-headless-linux-x64.tar.gz	Extract and follow docs/headless-linux.md

The macOS builds are signed and notarized with the UCSF Developer ID. The two
signed updater ZIPs and latest-mac.yml are also included for in-app updates.

Highlights

A steadier, more informative desktop

• Session history now appears immediately from a local cache and progressively
  reconciles with the daemon instead of blocking the view on a full fetch.
• Available updates live in a quiet sidebar action instead of interrupting work
  with a modal. macOS users on v1.86.0 or newer still get one-click restart and
  update.
• Generated file paths and supported URLs open directly in BioRouter's artifact
  preview, keeping the result and its originating conversation together.
• Editing a past message now creates one canonical divergence at the correct
  fork point, so branch lookup and replay remain consistent.
• Bundled tools have a clearer Capabilities surface in Settings, including
  permission inspection and configuration. Bundled local models also use names
  that distinguish the built-in Llama Server from Ollama.
• Usage Insights now includes durable per-model, per-day, cache-token, and
  month-to-date accounting. Partial or unknown pricing is labeled as incomplete
  rather than presented as a deceptively precise total.
• The home screen, Knowledge workspace, chat greetings, panels, tool cards,
  menus, tooltips, and compact window layouts were refined for quieter motion,
  complete controls, predictable wrapping, and responsive resizing. System
  Reduce Motion remains respected.

More controllable agent runs

• Per-reply wall-clock, token, and dollar budgets provide explicit limits for
  long agentic turns.
• Repetition, oscillation, repeated failures, and no-progress stalls are
  detected with staged soft-interrupt and hard-stop behavior instead of letting
  a loop run indefinitely.
• Reliable request-scoped cancellation, idempotent permission replies, and the
  restored soft-interrupt path make active work easier to stop without corrupting
  the session.
• Structured success checks, optional reflection and post-edit diagnostics,
  structured-output validation, persistent goals, living plans, active-work
  tracking, background subagent results, and shadow-git checkpoints improve
  recovery and make progress easier to inspect.
• Hooks can match tool input, rewrite requests before execution, block results
  afterward, and return aggregates. Permission rules can be scoped by directory
  and command prefix with clearer risk grades and call previews.
• Oversized messages and tool results use bounded previews and workspace-backed
  handles; context preparation now ranks injected material, preserves recent
  turns, validates compaction, and falls back progressively when a model window
  is exceeded.

Security and cross-platform hardening

• A central secret-redaction boundary and tool-output scanning reduce accidental
  credential, PII, and prompt-injection exposure.
• Shell execution uses an auditable command policy plus OS isolation: macOS
  Seatbelt and Linux Landlock/seccomp where available, with explicit behavior on
  Windows.
• ACP WebSocket authentication, app WebSocket origin checks, artifact-frame
  origins, rate limiting, secret comparison, Electron navigation, and external
  link handling were hardened.
• Shell working directories are validated before execution, Windows background
  processes receive graceful termination and PID-reuse protection, and native
  tests now preserve platform-specific paths, shells, hooks, and dependencies.
• One shared cross-compilation recipe now drives both CI and release builds.
  Cross-target Cargo outputs are isolated so simultaneous Linux and Windows
  builds cannot corrupt one another.

Faster chat, knowledge, and terminal rendering

• Desktop streaming batches text deltas to animation frames, and the terminal UI
  renders at a bounded frame rate instead of repainting for every token.
• Conversation repair and compaction avoid repeated full-history scans, while
  large transcripts share immutable data instead of copying it per turn.
• Knowledge search caches BM25 indexes and tree-sitter queries. MCP processes can
  be pooled across sessions, and desktop windows share a single daemon.
• Startup work for first-run skills and Soul installation moves to the
  background. Text-only replies skip unnecessary tool-response scans.
• The CLI/TUI keeps the v1.88.0 feature set aligned with desktop, including
  terminal chat, completion and model selection, usage reporting, diagnostics,
  web access, file-drop path handling, and biorouter doctor.

Agent Drafter and app SDK reliability

• The Agent Drafter contract is enforced throughout generation, validation,
  export, and runtime startup. Failures are visible, drag targets remain
  reachable, and generated apps are exercised by an executable smoke harness.
• The remediation work is grounded in a 100-app test drive and adds SDK
  integration, quality gates, standalone control-server hardening, safer app
  capabilities, and more dependable artifact previews.
• App SDK v2 and structured app output handling improve how generated tools
  declare capabilities, request permissions, and validate results.

Provider, model, and headless improvements

• GPT-5.6 model-family metadata is included, and each model carries its own
  context window so local and remote clients resolve capacity consistently.
• Cache-token capture and cache-aware pricing now cover Claude and Claude on
  Amazon Bedrock in addition to the broader usage-reporting pipeline.
• The browser-served headless package correctly rewrites code-split JavaScript,
  CSS, fonts, and other root-absolute assets when deployed behind a URL prefix.
• CLI-only and headless Linux distributions remain independent of Electron for
  server, HPC, container, and browser-only deployments.

Release verification

Before publication, the release artifacts are built from the v1.88.0 source and
run in their target environments. The gate covers:

• signed, notarized, and stapled Apple Silicon and Intel apps mounted from their
  DMGs, including packaged CLI/daemon version checks and desktop startup;
• Debian and RPM desktop installation, packaged CLI/daemon execution, and GUI
  startup under a virtual display;
• CLI-only Debian and RPM installation plus terminal entry-point checks;
• headless binary execution, browser bundle startup, health endpoint, and page
  fetch in a clean Linux container;
• Windows CLI, daemon, terminal entry point, and desktop startup on a native
  Windows GitHub-hosted runner;
• the complete desktop test suite, Rust CLI tests, version consistency, release
  architecture checks, and updater-manifest validation.

Upgrade notes

No configuration changes are required. macOS users on v1.86.0 or later can use
the in-app Restart & Update action. Everyone else can install the matching
package above over the current version.

BioRouter v1.87.1

Biorouter v1.87.1 Release Notes

Release Date: July 2026
Repository: github.com/BaranziniLab/biorouter

This is a UI-polish release on top of v1.87.0. It rolls out a warmer, calmer
two-tone desktop theme across every panel — a beige sidebar against an off-white
chat canvas, flatter cards and rows, hairline separators, and a chat composer
with a clearer edge. It also fixes the top-of-chat controls so they stay
clickable when the sidebar is collapsed. No breaking changes — existing installs
upgrade in place, and your settings, sessions, extensions, and knowledge bases
are preserved.

Downloads

Platform	File	Install
macOS (Apple Silicon)	BioRouter-1.87.1-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS (Intel)	BioRouter-1.87.1-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows (x64)	BioRouter-win32-x64-1.87.1.zip	Unzip and run BioRouter.exe
Linux Ubuntu / Pop!_OS (x64)	biorouter_1.87.1_amd64.deb	sudo dpkg -i biorouter_1.87.1_amd64.deb
Linux Fedora / RHEL (x64)	BioRouter-1.87.1-1.x86_64.rpm	sudo rpm -i BioRouter-1.87.1-1.x86_64.rpm
Linux — CLI only Ubuntu / Debian (x64)	biorouter-cli_1.87.1_amd64.deb	sudo apt install ./biorouter-cli_1.87.1_amd64.deb
Linux — CLI only Fedora / RHEL (x64)	biorouter-cli-1.87.1-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.87.1-1.x86_64.rpm

The two CLI-only packages install just the headless binaries (biorouter +
biorouterd) with no Electron/GUI payload — ideal for servers, HPC nodes, and
containers. (Local models need glibc ≥ 2.35 — Debian 12+/Ubuntu 22.04+.)

macOS builds are signed and notarized with the UCSF Developer ID certificate.
Users on v1.86.0 or later can update in place with the one-click "Restart &
Update" button — no need to re-download the DMG.

What's New

Warm two-tone desktop theme

The desktop app moves to a calmer, warmer palette. The sidebar now sits on its
own warm-beige surface against an off-white chat canvas, giving the window a
clear two-tone structure. The main panel squares off to sit flush with the
straight sidebar edge, and a hairline divider replaces the heavier separator.

Cards, list rows, and settings surfaces across Home, Apps, Workflows, Scheduler,
Settings, Skills, Extensions, and Knowledge were flattened to a consistent
token-based border system, so panels read as one product rather than a stack of
independently styled screens. Overlays, dropdowns, diagnostics, and the
onboarding provider cards were harmonized to match.

The chat composer gains a visible edge and a subtle lift (a dedicated shadow
token) so the input area stands out from the canvas without feeling heavy.

What's Fixed

Top controls stay clickable with the sidebar collapsed

When the sidebar was collapsed, the row of controls at the top of the chat
became unclickable and the session-name pill overlapped the collapse toggle.
The top controls are now correctly hit-testable when the sidebar is collapsed,
and the session-name pill is offset so it no longer sits under the toggle.

Upgrade Notes

No configuration changes are required. ~/.config/biorouter (your providers,
sessions, extensions, and knowledge bases) is untouched by the upgrade.

Changes Since v1.87.0

• Warm two-tone canvas: dedicated beige sidebar surface against an off-white
  chat canvas.
• Flattened cards and rows across Home, Apps, Workflows, Scheduler, Settings,
  Skills, Extensions, and Knowledge to a shared token border system.
• Main panel squared off to sit flush with the straight sidebar; hairline
  sidebar edge and a defined text-subtle token.
• Chat composer given a visible edge and a subtle-lift shadow token; overlays
  and dropdown menus harmonized.
• Settings header flattened with consistent section labels; Skills header inset
  divider; onboarding select-focus and extensions highlight refinements.
• Fixed top chat controls being unclickable and the session-name pill
  overlapping the toggle when the sidebar is collapsed.
• Landing site: added the BioRouter 1.87 release video and a BAAM skills /
  extensions expansion announcement.

---

Biorouter is built by the Baranzini Lab at UCSF. Learn more at biorouter.ucsf.edu.

BioRouter v1.87.0

Biorouter v1.87.0 Release Notes

Release Date: July 2026
Repository: github.com/BaranziniLab/biorouter

This release focuses on making BioRouter feel calmer, more readable, and more
trustworthy across the desktop app while also hardening the agent runtime,
knowledge ingestion, and release packaging flow. The chat, home, dashboard,
knowledge, settings, workflows, scheduler, extensions, skills, applications,
and history panels now share a more consistent layout system: centered readable
content, compact surfaces, softer shadows, flatter separators, and clearer hover
affordances.

Downloads

Platform	File	Install
macOS (Apple Silicon)	BioRouter-1.87.0-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS (Intel)	BioRouter-1.87.0-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows (x64)	BioRouter-win32-x64-1.87.0.zip	Unzip and run BioRouter.exe
Linux Ubuntu / Pop!_OS (x64)	biorouter_1.87.0_amd64.deb	sudo dpkg -i biorouter_1.87.0_amd64.deb
Linux Fedora / RHEL (x64)	BioRouter-1.87.0-1.x86_64.rpm	sudo rpm -i BioRouter-1.87.0-1.x86_64.rpm
Linux — CLI only Ubuntu / Debian (x64)	biorouter-cli_1.87.0_amd64.deb	sudo apt install ./biorouter-cli_1.87.0_amd64.deb
Linux — CLI only Fedora / RHEL (x64)	biorouter-cli-1.87.0-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.87.0-1.x86_64.rpm
Linux — Headless browser server Debian / Ubuntu (x64)	biorouter-headless-linux-x64.tar.gz	Extract on a Debian-based server and run with the headless setup flow in docs/headless-linux.md

macOS builds are signed and notarized with the UCSF Developer ID certificate.
The macOS ZIP assets are published for in-app updates through latest-mac.yml;
manual macOS downloads should use the DMG files.

The two CLI-only packages install just the command-line/server binaries
(biorouter + biorouterd) with no Electron/GUI payload. The headless browser
server archive packages biorouter, biorouterd, biorouter-headless, and
the static web UI so BioRouter can run on a Debian/Ubuntu server and be opened
from a browser without bundling Electron or local user credentials.

Highlights

Cohesive desktop UI polish

The main desktop panels now use consistent readable widths so text does not
stretch edge-to-edge on wide windows or collapse awkwardly on narrow ones.
Chat input surfaces, empty-state prompts, tool-call rows, toasts, find bars, and
sidebar controls were tuned together so they feel like one product rather than
separate panel implementations.

Clearer knowledge ingestion

The Knowledge page now supports a dedicated default model for out-of-conversation
knowledge work, including staged-file digestion and knowledge graph maintenance.
In-conversation knowledge queries still use the active chat model. The knowledge
panel also has clearer drag-and-drop, paste-text, selector, and graph layout
affordances.

More useful agent drafting

Agent Drafter now has stronger support for app layout requirements, workflow
planning, context-management decisions, downloads, sub-agent orchestration, and
security harness generation. The drafted agents are easier to inspect and safer
to run because their generated bundles include clearer runtime scaffolding and
guardrail behavior.

Runtime and observability hardening

The agent loop, extension manager, sandbox, scheduler, workflow generation,
provider registry, MCP surfaces, and observability paths were tightened for more
predictable behavior. Tool-call presentation is more human-readable by default
while preserving access to raw details when needed.

Headless Linux packaging

BioRouter now has a documented headless Linux release path for Debian/Ubuntu
servers. The release artifact is built locally, verified for profile-free
packaging, and can be deployed to a server that serves the browser UI while
running the BioRouter daemon on the server. Credentials remain runtime
configuration and are not packed into the release archive.

Upgrade Notes

No configuration migration is required. Existing providers, sessions,
extensions, skills, knowledge bases, and app settings continue to live under the
same BioRouter configuration directory.

---

Biorouter is built by the Baranzini Lab at UCSF. Learn more at biorouter.ucsf.edu.

BioRouter v1.86.1

Biorouter v1.86.1 Release Notes

Release Date: June 2026
Repository: github.com/BaranziniLab/biorouter

This is a polish-and-reliability release on top of v1.86.0. It fixes session
auto-naming so chats stop getting stuck on "New Session," restores rich
artifact rendering in the standalone Expand window, redesigns the
tool-permission (human-in-the-loop) confirmation card, and tidies the App SDK
and Agent Drafter copy. The CLI status line now counts extensions the same way
the GUI does. No breaking changes — existing installs upgrade in place, and your
settings, sessions, and extensions are preserved.

Downloads

Platform	File	Install
macOS (Apple Silicon)	BioRouter-1.86.1-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS (Intel)	BioRouter-1.86.1-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows (x64)	BioRouter-win32-x64-1.86.1.zip	Unzip and run BioRouter.exe
Linux Ubuntu / Pop!_OS (x64)	biorouter_1.86.1_amd64.deb	sudo dpkg -i biorouter_1.86.1_amd64.deb
Linux Fedora / RHEL (x64)	BioRouter-1.86.1-1.x86_64.rpm	sudo rpm -i BioRouter-1.86.1-1.x86_64.rpm
Linux — CLI only Ubuntu / Debian (x64)	biorouter-cli_1.86.1_amd64.deb	sudo apt install ./biorouter-cli_1.86.1_amd64.deb
Linux — CLI only Fedora / RHEL (x64)	biorouter-cli-1.86.1-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.86.1-1.x86_64.rpm

The two CLI-only packages install just the headless binaries (biorouter + biorouterd) with no Electron/GUI payload — ideal for servers, HPC nodes, and containers. (Local models need glibc ≥ 2.35 — Debian 12+/Ubuntu 22.04+.)

macOS users on v1.86.0 or later can update in place with the one-click "Restart & Update" button — no need to re-download the DMG.

What's Fixed

Sessions name themselves again

New chats were getting stuck on the placeholder "New Session" title. The
automatic LLM-generated rename was queued at the tail end of the reply stream,
but the streaming consumer stops as soon as the reply completes — so that tail
never ran and the naming call was never made. Renaming now happens right after
the reply loop ends, regardless of how the turn finished, so every conversation
gets a real title. A session that grew past its early naming window without a
name will now still get named once it keeps going, and the desktop app waits a
little longer for slower (reasoning-model) namers to land before giving up.

Rich artifacts render in the Expand window

Opening an Agent Drafter app or an Auto Visualiser figure in the
standalone "Expand" window showed a blank chart, a dead Convert button, or an
unresponsive embedded agent. The Expand window loads each artifact from a local
file but had inherited the app's strict script-src 'self' content-security
policy, which blocked the artifact's own inline scripts (Chart.js / D3 renders,
the converter's logic, the agentic runtime), the CDN chart libraries used in CDN
mode, and the WebSocket an embedded agent uses to reach its local sidecar. The
Expand window now applies a permissive policy scoped only to these
agent-generated, already-sandboxed artifacts (no Node access, isolated context);
everything else keeps the strict policy.

Redesigned tool-permission (human-in-the-loop) card

The permission prompt that appears when the agent asks to run a sensitive tool
has been rebuilt as one cohesive bordered card. It now has a lock-icon header
that clearly signals a permission request, consistent typography, a primary
Allow Once action, and a soft shadow with a gentle slide-in so you actually
notice the agent is waiting on you — replacing the old mismatched borderless
prompt stacked on a bordered button box.

Correct extension count in the CLI

The interactive CLI status line was counting the six foundational
capabilities (Developer, Extension Manager, Skills, Todo, Memory, Knowledge) as
extensions, so it showed "11 extensions" where the GUI shows 5. It now excludes
the capabilities (matching how the GUI categorizes them) and pluralizes
correctly, so "1 skill" reads singular and "0" / "2+" read plural across skills,
extensions, and knowledge bases.

What's Tidied

Cleaner App SDK & Agent Drafter copy

The App SDK settings section drops the "(experimental)" tag, and its four
safety-framework toggle descriptions were rewritten in plainer language. The
Agent Drafter extension description was likewise cleaned up. The
"Popular Chat Topics" suggested-prompt block has been removed from the
new-session screen for a calmer, less cluttered start.

Upgrade Notes

No configuration changes are required. ~/.config/biorouter (your providers,
sessions, extensions, and knowledge bases) is untouched by the upgrade.

---

Biorouter is built by the Baranzini Lab at UCSF. Learn more at biorouter.ucsf.edu.

BioRouter v1.86.0

Biorouter v1.86.0 Release Notes

Release Date: June 2026
Repository: github.com/BaranziniLab/biorouter

This is a feature-and-fix release. It adds one-click "Restart & Update" auto-update for macOS, multi-monitor screen capture with vision input, agent-readable UI-automation errors, and new built-in extension/skill authoring skills. It also adds a Capabilities settings section for foundational built-ins and hardens the Agent Drafter preview. No breaking changes — existing installs upgrade in place.

Downloads

Platform	File	Install
macOS (Apple Silicon)	BioRouter-1.86.0-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS (Intel)	BioRouter-1.86.0-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows (x64)	BioRouter-win32-x64-1.86.0.zip	Unzip and run BioRouter.exe
Linux Ubuntu / Pop!_OS (x64)	biorouter_1.86.0_amd64.deb	sudo dpkg -i biorouter_1.86.0_amd64.deb
Linux Fedora / RHEL (x64)	BioRouter-1.86.0-1.x86_64.rpm	sudo rpm -i BioRouter-1.86.0-1.x86_64.rpm
Linux — CLI only Ubuntu / Debian (x64)	biorouter-cli_1.86.0_amd64.deb	sudo apt install ./biorouter-cli_1.86.0_amd64.deb
Linux — CLI only Fedora / RHEL (x64)	biorouter-cli-1.86.0-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.86.0-1.x86_64.rpm

The two CLI-only packages install just the headless binaries (biorouter + biorouterd) with no Electron/GUI payload — ideal for servers, HPC nodes, and containers. (Local models need glibc ≥ 2.35 — Debian 12+/Ubuntu 22.04+.)

What's New

One-click "Restart & Update" (macOS)

Updating no longer means opening the download page, grabbing the DMG, and dragging to Applications. A single button now downloads the new release in the background and, on click, restarts Biorouter on the new version in place. Your settings, sessions, and extensions are preserved — only the app bundle is swapped; ~/.config/biorouter is untouched. Both the update modal and the Settings update section drive the same one-click flow with a live progress bar. The release pipeline now also ships the signed zips and a latest-mac.yml manifest that the updater needs.

Multi-monitor capture + vision input

The Computer Controller and Developer screen-capture tools now enumerate connected displays (index, name, resolution, position, scale, primary) on macOS, Linux, and Windows, so a multi-monitor setup can re-capture any screen by index, and list_windows accepts a window-title substring. Xiaomi MiMo (v2.5 / v2) is now declared image-capable, so it can consume screenshots like the Anthropic and OpenAI vision providers.

Extension / skill authoring skills

develop-biorouter-extension and develop-biorouter-skill are now real built-in SKILL.md skills for authoring Biorouter extensions and skills.

Capabilities — on by default, managed in one place

The foundational built-ins — Developer, Extension Manager, Skills, Todo, Memory, Knowledge — are now first-class Capabilities in Settings, enabled by default:

• Default-enabled on upgrade. If you upgraded from an older build where some of these were left off, this version turns them back on for you (once) so the agent has its core abilities out of the box. You can still disable any of them in Settings → Capabilities, and that choice sticks.
• Out of the chat extension list. Capabilities no longer clutter the per-conversation extension dropdown in the chat box and the dashboard — that list now shows only the optional built-ins and the extensions you install yourself. Capabilities are toggled only in Settings, where they belong.

Agent reliability

Backend agent-loop improvements (shared by the CLI and the desktop app), found while stress-testing the agent across 100 real multi-file projects:

• Continue-on-truncation. When a provider cuts a response off at its output-length limit (finish_reason="length") with no tool call, the agent auto-continues the turn instead of stopping on a half-written response — gated strictly on the explicit length signal and bounded so it can't loop.
• No more "keep going" loops when stuck. An earlier mid-task "keep working until your todos are done" nudge could repeat itself when the agent was genuinely blocked (e.g. an unrecoverable provider error) without resolving the cause. That hard-coded nudge is removed; "don't stop while work is unfinished" is now handled only by the bounded, user-configurable Stop-hook and /goal mechanisms (which give up when progress stalls).
• The turn-ending finish_reason is surfaced in the logs, so "finished" vs "cut off" is distinguishable.

CLI quality-of-life (interactive TUI)

• Scroll the whole conversation. The mouse wheel now scrolls the conversation history instead of the terminal's own buffer (which used to expose the pre-launch banner). Native text selection still works with your terminal's bypass modifier (Option on macOS Terminal/iTerm2, Shift elsewhere); PageUp/PageDown scroll too.
• Tidier tool output. As tool calls pile up, older tool results collapse to a one-line summary so only the current result stays expanded — the conversation no longer gets buried under walls of old output.
• See your queued messages. Messages you type while the agent is working now appear in full in a "queued" pane (not just a count), so you always see what runs next, in order.

MiMo vision fix

Only the multimodal mimo-v2-omni model is now advertised as image-capable; the text MiMo models (which reject image input) no longer get fed screenshots — and, defensively, image content is stripped from requests to a non-vision MiMo model. This fixes a stuck loop where a screenshot/vision step would 404 (No endpoints found that support image input) and strand the agent.

What's Fixed

• UI automation: failing osascript / PowerShell scripts now surface as real tool errors with stderr and exit status (instead of a fake "success" that made the model retry blindly), and are guarded against long hangs.
• Code execution: binary/blob resources (e.g. Auto Visualiser ui:// HTML blobs) are collected out-of-band and appended for inline UI rendering, with no duplicate payload for text resources.
• Agent Drafter: preview auto-resize, in-app chat protocol, and sandbox-safe send.

Upgrading

No action required beyond installing the new build for your platform from the table above. Settings, sessions, knowledge bases, and configured providers are preserved. On macOS, in-app "Restart & Update" handles the swap for you.

Changes Since v1.85.4

• feat: multi-monitor capture + vision input, agent-readable UI-automation errors, dev skills
• feat(updater): one-click "Restart & Update" auto-update for macOS
• feat(settings): add Capabilities section for foundational built-ins
• fix(agent-drafter): preview auto-resize, in-app chat protocol, sandbox-safe send
• feat(agent): continue-on-truncation when a turn is cut off at the output-length limit
• feat(agent): log finish_reason at turn-end (done-vs-stopped observability)
• feat(capabilities): default-enable foundational capabilities on upgrade; hide them from the chat extension dropdown (managed in Settings)
• fix(agent): remove the hard-coded "unchecked todos" continuation that could loop when the agent was stuck; defer to the bounded Stop-hook / /goal mechanisms
• fix(providers/mimo): advertise vision only for mimo-v2-omni; strip image content from requests to text-only MiMo models (fixes the image-404 stuck loop)
• feat(cli/tui): mouse-wheel scrolls the conversation; collapse older tool outputs; show queued messages in full

BioRouter v1.85.4

Biorouter v1.85.4 Release Notes

Release Date: June 2026
Repository: github.com/BaranziniLab/biorouter

This is a feature-and-fix release. It adds the Agent Drafter built-in extension for authoring AI-agent-enabled artifacts, an ACP WebSocket transport, two new LLM providers (z.ai / GLM and Xiaomi MiMo), 24 new Auto Visualiser charts, and broader tree-sitter language support (C++, C, R, Julia, MATLAB). It also hardens the interactive CLI, the developer extension, and provider retries. No breaking changes — existing installs upgrade in place.

Downloads

Platform	File	Install
macOS (Apple Silicon)	BioRouter-1.85.4-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS (Intel)	BioRouter-1.85.4-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows (x64)	BioRouter-win32-x64-1.85.4.zip	Unzip and run BioRouter.exe
Linux Ubuntu / Pop!_OS (x64)	biorouter_1.85.4_amd64.deb	sudo dpkg -i biorouter_1.85.4_amd64.deb
Linux Fedora / RHEL (x64)	BioRouter-1.85.4-1.x86_64.rpm	sudo rpm -i BioRouter-1.85.4-1.x86_64.rpm
Linux — CLI only Ubuntu / Debian (x64)	biorouter-cli_1.85.4_amd64.deb	sudo apt install ./biorouter-cli_1.85.4_amd64.deb
Linux — CLI only Fedora / RHEL (x64)	biorouter-cli-1.85.4-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.85.4-1.x86_64.rpm

The two CLI-only packages install just the headless binaries (biorouter + biorouterd) with no Electron/GUI payload — ideal for servers, HPC nodes, and containers. (Local models need glibc ≥ 2.35 — Debian 12+/Ubuntu 22.04+.)

What's New

Agent Drafter

A new built-in Agent Drafter MCP extension lets you author AI-agent-enabled artifacts directly in Biorouter. Drafts render with native Biorouter aesthetics, support agent-sizable and expandable previews, and run as working standalone agents. The accompanying ACP WebSocket transport improves multi-agent orchestration and fixes extension discoverability.

New LLM providers

z.ai (GLM) and Xiaomi MiMo are now selectable LLM providers. DeepSeek's deepseek-chat / deepseek-reasoner aliases are future-proofed against retirement.

Richer Auto Visualiser

The Auto Visualiser pipeline is hardened and gains 24 new visualizations spanning charts, scientific plots, relationship/hierarchy diagrams, Mermaid diagrams, and geo maps.

More languages in the analyze extension

tree-sitter is bumped to 0.26, adding C++, C, R, Julia, and MATLAB to the analyze extension's supported languages.

CLI / TUI overhaul

The interactive CLI gains wrapping input, a bottom-pinned input bar, live streaming, and richer rendering.

What's Fixed

• CLI: --resume now falls back gracefully when a session can't be restored, and tool-call paths render readably.
• Agent: the per-turn action-limit stop is now explicit and quantified.
• Developer extension: adds git context, a verify/checkpoint Stop hook, and accepts file_path as an alias for the text editor's path argument.
• Providers: a deeper retry budget for transient rate-limit (429) errors.
• Auto Visualiser: accepts stringified data arguments, fixes map sizing, and drops the experimental note.

Upgrading

No action required beyond installing the new build for your platform from the table above. Settings, sessions, knowledge bases, and configured providers are preserved.

Changes Since v1.85.3

• feat(mcp,acp): Agent Drafter built-in extension + ACP WebSocket transport, native aesthetics and standalone agents
• feat(providers): add z.ai (GLM) and Xiaomi MiMo; future-proof DeepSeek aliases
• feat(mcp/autovisualiser): harden the pipeline and add 24 new visualizations
• feat(mcp/analyze): tree-sitter 0.26 — add C++, C, R, Julia, MATLAB
• feat(cli/tui): wrapping input, bottom-pinned bar, live streaming, richer rendering
• fix(cli,agent,developer,providers): graceful --resume, quantified action-limit stop, developer git context + file_path alias, deeper 429 retry budget

BioRouter v1.85.3

Biorouter v1.85.3 Release Notes

Release Date: June 2026
Repository: github.com/BaranziniLab/biorouter

This is a polish-and-fix release. Chat now defaults to autonomous tool-calling, the Llama Server context window is reported accurately across the CLI and GUI, and the interactive CLI gains clean streaming and copy/paste. It also fixes the perpetual "Biorouter CLI Update" prompt with a more resilient installer. No breaking changes — existing installs upgrade in place.

Downloads

Platform	File	Install
macOS (Apple Silicon)	BioRouter-1.85.3-arm64.dmg	Open the DMG and drag BioRouter.app to /Applications
macOS (Intel)	BioRouter-1.85.3-x64.dmg	Open the DMG and drag BioRouter.app to /Applications
Windows (x64)	BioRouter-win32-x64-1.85.3.zip	Unzip and run BioRouter.exe
Linux Ubuntu / Pop!_OS (x64)	biorouter_1.85.3_amd64.deb	sudo dpkg -i biorouter_1.85.3_amd64.deb
Linux Fedora / RHEL (x64)	BioRouter-1.85.3-1.x86_64.rpm	sudo rpm -i BioRouter-1.85.3-1.x86_64.rpm
Linux — CLI only Ubuntu / Debian (x64)	biorouter-cli_1.85.3_amd64.deb	sudo apt install ./biorouter-cli_1.85.3_amd64.deb
Linux — CLI only Fedora / RHEL (x64)	biorouter-cli-1.85.3-1.x86_64.rpm	sudo dnf install ./biorouter-cli-1.85.3-1.x86_64.rpm

The two CLI-only packages install just the headless binaries (biorouter + biorouterd) with no Electron/GUI payload — ideal for servers, HPC nodes, and containers. (Local models need glibc ≥ 2.35 — Debian 12+/Ubuntu 22.04+.)

What's New

Autonomous-by-default chat

Chat now defaults to Autonomous tool-calling, and the smart/autonomous mode dropdown has been removed from the chat box and dashboard rows. The mode remains fully configurable under Settings → Chat. The Workflow and Diagnostics buttons are now grouped beside the model selector, and a terminal launcher sits next to the working-directory switcher — launching the CLI rooted in the chat's working directory (on macOS, via Terminal.app directly).

update-soul skill

The built-in soul-writer skill has been renamed to update-soul with a proper description, and the legacy directory is removed on startup so upgraded users no longer see a duplicate. The Skills UI frontmatter parser also now handles YAML block scalars (folded > / literal |) and quoted values, so multi-line descriptions render as text instead of a literal >- indicator.

What's Fixed

• Llama Server context window: the reported context window is now correct and consistent across surfaces. Biorouter reads the running model's real window from llama-server's /props (probing the configured port even for a server this process didn't start), so the CLI gauge and GUI status agree. The fixed 32k default is replaced with a memory-tiered default (≥64 GB → 128k, ≥32 GB → 64k, ≥16 GB → 32k, else 16k, capped at 128k); LLAMACPP_CONTEXT_SIZE unset or 0 means auto, a positive value pins it.
• CLI install: install_cli now overwrites the binary that is actually first on PATH instead of dropping a copy in a shadowed directory — fixing the perpetual "Biorouter CLI Update" prompt caused by a stale on-PATH copy winning the PATH race. The dependency setup modal re-probes after install and reports the exact stale path to remove. Installers are now non-interactive (rustup -y; winget --accept-*-agreements --disable-interactivity) so they don't hang, and llama-server and Rust were added to the native dependency checks.
• CLI TUI streaming & copy/paste: per-token streaming deltas are coalesced into whole messages before rendering, so prose, tables, and lists no longer shatter into one fragment per line (and the context-window meter no longer races up). Markdown word-wrap is smarter (hard-wrapping over-wide non-URL tokens while keeping URLs intact, preserving inline ANSI styling across breaks, and shrinking wide tables to fit narrow terminals). Copy/paste now works in the TUI — the mouse is no longer captured, so native text selection is restored (scrolling stays on PageUp/PageDown).
• Settings polish: tightened vertical spacing across settings sections and the grouped extension-loading toast, and status indicators now render as round dots.

Upgrading

No action required beyond installing the new build for your platform from the table above. Settings, sessions, knowledge bases, and configured providers are preserved. If you previously saw a recurring "Biorouter CLI Update" prompt in the desktop app, this release's installer fix resolves it by updating the binary that is actually first on your PATH.

Changes Since v1.85.2

• feat(cli,ui): autonomous-by-default chat, CLI streaming/copy-paste fixes, update-soul skill, resilient CLI install
• fix(llamacpp): report the model's real context window, with a memory-tiered default
• style(ui): settings spacing + round status indicators