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3.2 RC2 Release Notes

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Frédéric Clavert edited this page Jul 24, 2026 · 6 revisions

v1.0.0-rc.2 — Release Notes

Release date: May 2026 Tag: v1.0.0-rc.2

RC2 is the first release after the ClioBrain fusion — the standalone ClioBrain project (now archived) has been absorbed into ClioDeck as the new Brainstorm mode. RC2 also ships an MCP server, three archive connectors (Europeana / Gallica / HAL), and Obsidian vault as a RAG source.

The strategy and implementation plan that drove the fusion live in docs/archive/fusion-cliobrain-strategy.md and docs/archive/fusion-cliobrain-implementation-plan.md — commits on this branch reference the step numbers defined there.

What's new

1. Brainstorm mode (ClioBrain fusion)

ClioDeck now has a dedicated chat mode for the exploratory phase of research, sitting between the corpus panels and the Write WYSIWYG editor. Highlights:

  • Streamed chat through the typed ProviderRegistry (5 providers: Ollama, OpenAI-compatible, Anthropic, Mistral, Gemini).
  • Agent loop with MCP tool-use (any MCP client you've configured contributes its tools).
  • .cliohints injection — a workspace-level system-prompt fragment from .cliodeck/hints.md.
  • Context compaction sized to the active model (keeps system + recent turns verbatim, summarises the middle).
  • First-class AbortController cancellation per session.

The legacy RAG chat is still wired for safety; RC3 will deepen Brainstorm and retire it.

See: Brainstorm Mode Guide.

2. MCP integration (both directions)

ClioDeck speaks the Model Context Protocol as both a client and a server.

  • MCP clients (Settings → MCP Clients) — register stdio or SSE MCP servers. Their tools become callable by the LLM inside a Brainstorm turn. Each client exposes a typed state machine (unconfigured | spawning | handshaking | ready | degraded | failed | stopped), not a connected boolean; partial success is first-class.
  • MCP server (Settings → MCP Server) — toggles a bin/cliodeck-mcp binary that exposes the workspace's corpus to Claude Desktop, Claude Code, or any other MCP client. Off by default. Every call is appended to .cliodeck/mcp-access.jsonl as a typed event. The Settings panel generates ready-to-paste snippets for Claude Desktop, Claude Code CLI, and Generic MCP (stdio) clients.

The server exposes 9 tools: search_documents, search_obsidian, search_tropy, search_zotero, graph_neighbors, entity_context, search_gallica, search_hal, search_europeana.

See: MCP Integration Guide.

3. Archive connectors — Gallica, HAL, Europeana

Three public-archive connectors are wired as MCP tools on the built-in server:

  • Gallica (BnF) — SRU public endpoint, no key.
  • HAL (CCSD) — Solr public endpoint, no key.
  • Europeana — REST, requires a free wskey. Configure in Settings → Archives.

API keys are stored via Electron's safeStorage (OS keychain on macOS, libsecret on Linux, DPAPI on Windows) — never in config.json. The Europeana key is read at call time from EUROPEANA_API_KEY, so it can be rotated without a restart.

See: Archive Connectors Guide.

4. Obsidian vault as RAG source

ClioDeck can point at an Obsidian vault folder, index the notes inside, and treat them as a first-class source alongside PDFs (secondary) and Tropy archives (primary):

  • Wikilinks, tags and frontmatter parsed.
  • Indexed into the shared .cliodeck/brain.db (obsidian_*-prefixed tables), alongside PDF and Tropy vectors — not a separate obsidian-vectors.db file, even at this tag.
  • Reachable from Brainstorm as the notes source-type and from external MCP clients via search_obsidian.
  • Partial-success reporting (indexed / skipped / failed).

See: Obsidian Vault Guide.

5. Settings panel UX

  • All Settings sections are now collapsible (CollapsibleSection wrapper) so the Expert mode stops being a wall of forms.
  • Settings has Simple / Expert tabs — beginner-facing essentials by default, full surface on demand.
  • Archives section fully internationalised (FR / EN).

Workspace layout changes

The workspace is now flat — the previous nested .cliodeck/v2/* layout has been collapsed:

<project>/.cliodeck/
  brain.db                  # consolidated SQLite: PDFs, Tropy primary sources, research history, AND Obsidian vault vectors
  config.json               # schema_version: 2
  hints.md                  # .cliohints workspace context
  recipes/, recipes-runs/
  mcp-access.jsonl          # MCP server audit log
  security-events.jsonl     # source-inspector events

ClioDeck auto-migrates the older nested layout (.cliodeck/v2/*), pre-fusion v1 layouts, and bare .cliobrain/ workspaces on project load — no manual action required (migrateWorkspaceToFlat in backend/core/workspace/migrator.ts). By this release, the db-fusion was already complete — and further along than an earlier version of this page said. It's not just vectors.db (PDFs) and primary-sources.db (Tropy) folded into brain.db: obsidian-vectors.db was folded in too, 5 days before this tag was cut (c044d42, verified an ancestor of v1.0.0-rc.2 via git merge-base --is-ancestor; obsidianStorePath() already returned the brain.db path at this exact tag). The migrator already renames the legacy vault tables in place (notes→obsidian_notes, chunks→obsidian_chunks, …) to avoid colliding with the PDF/Tropy tables sharing the same file. None of these four legacy files coexist as separate files at RC2.

Bug fixes worth calling out

  • RAG / BM25. Short acronyms (e.g. KAQG, CIA) are now boosted on the exact-match path. Hybrid search takes max(dense, sparse-synthetic) so BM25 hits no longer get drowned by semantic neighbours. BM25-only hits are surfaced through the grounding prompt instead of being silently dropped.
  • Chat. num_ctx is plumbed end-to-end; gemma3 / gemma4 families are recognised on the Ollama provider. Chat-engine logs the resolved model name (not the provider's display name).
  • PDF indexing. Worker drains stdout before exit so large payloads don't get truncated. PDF re-index for Zotero-only citations is repaired. Embedding input is capped to avoid Ollama 500s on outsized chunks. Packaged app probes Homebrew/nvm Node paths so it can find a Node runtime to index PDFs.
  • Journal. Resolved model name is written into the AI-operation log. Sessions reload + error state clears when a project opens.

Known issues / limitations

  • Pre-existing test failures. 21 tests fail under Vitest because of better-sqlite3 native bindings; Ollama live-backend tests time out when no Ollama is running. None of these affect the runtime.
  • No React component tests yet. jsdom + @testing-library/react setup is pending.
  • Brainstorm UX is inherited. The chat panel is still the legacy shape. RC3 will rework it (parallel scratch threads, branching, tool-call surfacing).
  • Per-tool toggle UI is minimal. Brainstorm can filter the MCP tool catalog (enabledTools) but the renderer surface for this is bare-bones.
  • Recipes export step. document_id was already honored at this tag (contrary to an earlier version of this page, which claimed it was ignored) — the real limitation was that pdfExportService.exportToPDF() was called with projectType: 'article' hardcoded, so a recipe run inside a book project exported a single file rather than the assembled manuscript. Fixed before RC3 (src/main/services/recipe-step-handlers.ts now reads the real project type from project.json and calls assembleManuscript() for books).
  • Ollama tool capability is whitelisted. Only ministral-3:8b/14b, qwen3:8b/14b/32b, mistral-nemo advertise tool-use. Llama 3.x / 4.x families get tools: false. See OLLAMA_TOOL_CAPABLE_PATTERNS in backend/core/llm/providers/ollama.ts and docs/archive/research-ollama-tools-1.8.md.

Upgrade notes

  • From RC1. Open your project — flat-layout migration runs automatically. No data loss; the previous v2/ directory is replaced in place.
  • From ClioBrain. Migration is automatic on project load — migrateWorkspaceToFlat detects a .cliobrain/ workspace (MigrationKind = 'cliobrain') and copies canonical artifacts into the flat .cliodeck/ layout. Vault path, notes index and chat history carry over.

The fusion branch (feat/fusion-cliobrain) was ~190 commits ahead of main when it merged at this tag; it has since been merged and deleted, its history preserved on main.

What's next (RC3)

Deeper Brainstorm work: parallel scratch threads, branching turns, better tool-call surfacing, the per-tool toggle UI, and the long-postponed retirement of the legacy chat service. Plus continued polish on the RAG retrieval pipeline.

Documentation

For older release notes and implementation plans, see the archive folder.

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