@andespindola/brainlink 0.1.0-beta.13 → 0.1.0-beta.131

package/AGENTS.md

@@ -6,19 +6,19 @@ This file tells coding agents and AI assistants how to use this repository.
 
 Brainlink is a local-first knowledge memory for agents.
 
-It reads a Markdown vault, extracts `[[wiki links]]` and `#tags`, builds a local SQLite full-text index, and returns compact context packages that agents can inject into prompts.
+It reads a Markdown vault, extracts `[[wiki links]]` and `#tags`, builds a local file index at `.brainlink/index.json`, and returns compact context packages that agents can inject into prompts.
 
 ## Source Of Truth
 
 Markdown files are the source of truth.
 
-The SQLite database at `.brainlink/brainlink.db` is a derived index. It can be deleted and rebuilt with:
+The JSON index at `.brainlink/index.json` is derived. It can be deleted and rebuilt with:
 
 ```bash
 npm run dev -- index --vault ./vault
 ```
 
-Do not store permanent knowledge only in SQLite.
+Do not store permanent knowledge only in index artifacts.
 
 By default, the installed Brainlink CLI uses `$HOME/.brainlink/vault` as its vault. Passing `--vault` or setting `vault` in `brainlink.config.json` intentionally selects a custom vault such as `./vault`.
 
@@ -83,6 +83,9 @@ Use watch mode while editing notes:
 ```bash
 npm run dev -- server --vault ./vault --watch
 npm run dev -- watch --vault ./vault
+npm run dev -- bench --vault ./vault
+npm run dev -- bench --vault ./vault --watch
+npm run dev -- pack-backup --vault ./vault
 ```
 
 Start MCP over stdio:
@@ -107,10 +110,10 @@ npm run dev -- doctor --vault ./vault
 
 - Keep domain rules in `src/domain`.
 - Keep use cases in `src/application`.
-- Keep filesystem and SQLite details in `src/infrastructure`.
+- Keep filesystem and index details in `src/infrastructure`.
 - Keep CLI concerns in `src/cli`.
 - Prefer pure functions for parsing, ranking, formatting, and transformation.
-- Do not make SQLite the canonical storage layer.
+- Do not make index artifacts the canonical storage layer.
 - Do not add comments with emojis.
 - Keep JSON output backwards compatible where possible.
 

package/CHANGELOG.md

@@ -22,6 +22,30 @@
 - Added short-lived hybrid search cache with automatic invalidation on index changes.
 - Added `stats --extended` observability output with storage, quality and latency probes.
 - Added `docs/QUICKSTART.md` and aligned README/agent docs with the latest CLI/MCP flows.
+- Added middle-out context assembly so chunk selection expands around the strongest note chunk.
+- Added compressed-space pack prefiltering (token bloom index) before `.blpk` decryption and scan.
+- Improved graph UI auto-fit and viewport recovery so loaded nodes are re-centered when zoom/pan drifts to empty canvas.
+- Added cross-platform native desktop GUI auto-open for `blink server` (macOS Swift/WebKit, Windows PowerShell WinForms, Linux Python GTK/WebKit2), with app-window/browser fallback.
+- Changed Linux default UI launch to app-window/browser for lighter startup; Linux native GUI is now opt-in via `BRAINLINK_LINUX_NATIVE_GUI=1`.
+- Added native GUI parent-process monitoring so GUI windows close automatically when `blink server` stops.
+- Improved non-mac browser detection fallback to try installed Edge/Chrome/Firefox/Chromium candidates before system default open.
+- Improved graph filter rendering to keep hub anchor nodes visible (`Memory Hub`/`MOC`/high-degree fallback) for coherent relationship context.
+- Fixed graph modal content loading by correcting agent query parameter composition for `/api/graph-node` and `/api/graph-filter` requests.
+- Improved 50k+ graph rendering performance with viewport-aware spatial node culling, cached render visibility, and node-adjacent edge selection to avoid full graph scans every frame.
+- Added incremental vault indexing with file snapshots to reuse unchanged documents/chunks/embeddings, plus adaptive search-pack rebuild thresholds to avoid full re-compression on small edits.
+- Reduced large-graph HTTP payload size with compact `/api/graph-layout` encoding for high-node vaults and capped transmitted edges to improve UI load responsiveness.
+- Added aggressive graph LOD clustering when zoomed out, dynamic per-zoom edge render budgets, and a dedicated frontend worker for off-main-thread graph filter matching.
+- Improved Linux browser fallback launch stability by auto-applying Chromium compatibility flags (`--ozone-platform=x11`, `--disable-gpu`, `--disable-features=Vulkan,VaapiVideoDecoder`, `--disable-background-networking`) for app-window/browser modes.
+- Improved massive-graph UI responsiveness with stricter render budgets, adaptive heavy-graph frame throttling, reduced interaction hit-test frequency, and URL-first agent selection on initial graph load.
+- Improved 50k+ graph LOD behavior so zoomed-out views render lightweight cluster overviews and progressively reveal nodes/edges only as zoom increases.
+- Added `blink bench` with realtime index phase telemetry and per-run compressed-pack analysis (input/output bytes, ratio, saved space, rebuild reason and duration), including continuous watch mode.
+- Added tunable single-stage search-pack compression settings (`searchPack.rowChunkSize`, `searchPack.compressionLevel`, `searchPack.useDictionary`).
+- Added benchmark guardrails for compression savings and latency regression (`searchPack.guardrailMinSavingsPercent`, `searchPack.guardrailMaxLatencyRegressionPercent`), reported in `blink bench`.
+- Added `blink pack-backup` for offline second-stage compression backups of encrypted `.blpk` packs, outside the online query path.
+- Hardened Linux browser launch flags for Ubuntu 26 Chromium/Wayland compatibility (`--disable-vulkan`, `--use-gl=swiftshader`, `--ozone-platform-hint=x11`).
+- Improved pack resilience by auto-repairing missing search-pack manifests from existing `.blpk` files, avoiding unnecessary full repacks on small incremental updates.
+- Updated Linux graph auto-open behavior to prioritize the system default browser (`xdg-open`) before explicit browser fallbacks.
+- Removed implicit Chromium dependency in Linux auto-open flow; app-window launch is now opt-in (`BRAINLINK_LINUX_APP_WINDOW=1`).
 
 ## 0.1.0-beta.3
 
@@ -49,8 +73,8 @@
 ## 0.1.0-alpha.0
 
 - Added local-first Markdown vault indexing.
-- Added SQLite FTS, local semantic retrieval, wiki links, backlinks and graph retrieval.
-- Added SQLite semantic bucket indexing to narrow vector candidates for larger vaults.
+- Added local full-text indexing, local semantic retrieval, wiki links, backlinks and graph retrieval.
+- Added semantic candidate bucket indexing to narrow vector candidates for larger vaults.
 - Optimized title/link resolution with precomputed agent-scoped title maps.
 - Added CLI, JSON output, HTTP API and graph UI.
 - Added vault diagnostics: stats, broken links, orphans, validation and doctor.

package/CONTRIBUTING.md

@@ -22,7 +22,7 @@ npm run pack:smoke
 ## Design Rules
 
 - Markdown files are the source of truth.
-- SQLite is a derived index and must remain rebuildable.
+- Local index artifacts are derived and must remain rebuildable.
 - Domain parsing, graph analysis and layout should stay pure and testable.
-- CLI, HTTP, filesystem and SQLite code are adapters around application use cases.
+- CLI, HTTP, filesystem and index code are adapters around application use cases.
 - MCP integration should live outside this package by wrapping the CLI with `--json`.

package/COPYRIGHT.md

@@ -0,0 +1,5 @@
+Copyright (c) 2026 Substructa
+
+This project is licensed under the MIT License.
+
+See [LICENSE](./LICENSE) for full terms.

package/README.md

@@ -52,14 +52,15 @@ LLMs do not have infinite context. Brainlink gives agents an external memory lay
 1. Durable knowledge is written as Markdown.
 2. Notes are connected with `[[wiki links]]`.
 3. Concepts are classified with `#tags`.
-4. Brainlink builds a local SQLite index with FTS records and local embeddings.
+4. Brainlink builds a local JSON index (`.brainlink/index.json`) and private encrypted search packs.
 5. Agents query the index before responding.
 6. Brainlink returns compact, source-backed context.
 
-Markdown is the source of truth. `.brainlink/brainlink.db` is only a rebuildable index.
-Brainlink now keeps an automatic rollback snapshot at `.brainlink/brainlink.db.backup` plus rotating snapshots in `.brainlink/brainlink.db.backup.snapshots/`. If the main SQLite file is corrupted, Brainlink automatically restores the newest valid snapshot (or recreates a clean index when no snapshot exists).
-After each index run, Brainlink also writes private encrypted search packs at `.brainlink/search-packs/*.blpk`. If SQLite is unavailable, search falls back to these packs automatically.
+Markdown is the source of truth. `.brainlink/index.json` is a rebuildable index artifact.
+After each index run, Brainlink also writes private encrypted search packs at `.brainlink/search-packs/*.blpk` to preserve fast retrieval and portable recovery.
+Online retrieval always uses a single compression stage per pack; optional second-stage compression is reserved for offline backup artifacts only.
 Pack decryption uses a Brainlink key from `$BRAINLINK_HOME/keys` or from `BRAINLINK_SEARCH_PACK_KEY` when explicitly configured.
+Legacy `.jsonl.gz` packs are upgraded to `.blpk` automatically on first search/context access.
 
 ## Features
 
@@ -67,8 +68,12 @@ Pack decryption uses a Brainlink key from `$BRAINLINK_HOME/keys` or from `BRAINL
 - Obsidian-compatible `[[wiki links]]` and `#tags`.
 - Weighted graph edges so agents can rank relationship importance and priority.
 - Backlinks, broken-link reports, orphan detection and validation.
-- Full-text, semantic and hybrid retrieval modes.
-- SQLite-backed semantic candidate buckets for larger vaults.
+- Full-text, semantic and hybrid retrieval on a local file index.
+- Middle-out context assembly around the strongest chunk per document.
+- In-process index and context caching with automatic invalidation on index updates.
+- Compressed-space prefiltering for `.blpk` packs before decryption and scan.
+- Incremental indexing that reprocesses only changed markdown files and reuses existing chunks/embeddings for unchanged notes.
+- Adaptive compressed-pack rebuild policy to keep indexing fast during small edit batches.
 - Agent namespaces under `agents/<agent-id>/`.
 - S3-compatible bucket vaults through `s3://bucket/prefix` URIs.
 - CLI with machine-readable `--json` output.
@@ -76,6 +81,17 @@ Pack decryption uses a Brainlink key from `$BRAINLINK_HOME/keys` or from `BRAINL
 - Built-in MCP stdio server for agent tool integration.
 - Local HTTP API.
 - Realtime graph UI with agent selector and colored knowledge groups.
+- Graph renderer optimized for large datasets with viewport-driven node culling and edge lookup by visible nodes.
+- Canvas graph rendering uses the same batched node and edge pipeline for every graph size, reducing per-frame draw calls while keeping selected and hovered items highlighted.
+- WebGL acceleration is used when available for dense node and edge drawing, with Canvas 2D preserved as the interaction and fallback layer.
+- Graph rendering keeps the flat node scene and adds stable hierarchical mesh groups for vaults above 1000 notes, with every visible graph level filled toward 1000 nodes, each group capped at 1000 child nodes, and recursive parent groups when a level itself exceeds 1000 groups.
+- Large graph layout API automatically uses compact payload encoding with link-coverage-aware edge selection to reduce initial client load without hiding major relationships.
+- Large-segment layout spacing now grows logarithmically to keep initial visual density consistent between medium and very large vaults (for example, ~1k vs ~50k notes).
+- Graph coordinates are visually compacted across graph sizes so reset starts from a stable fitted scene and zoom-in progressively reveals local detail.
+- Zoomed-out graph LOD renders hierarchy groups as sparse relationship graph nodes and expands a group from the focused node's current viewport position only after it is framed, progressively hiding sibling groups in micro view.
+- Graph reset fits the full graph scene instead of starting in a separate macro overview mode.
+- Graph filtering runs in a dedicated browser worker to keep the UI thread responsive during heavy datasets.
+- Edge rendering budgets adapt to zoom level to prevent frame spikes on large graph panoramas.
 
 ## Install
 
@@ -285,7 +301,7 @@ export BRAINLINK_S3_FORCE_PATH_STYLE=1
 
 Bucket vaults mirror Markdown into a local cache under
 `$BRAINLINK_HOME/bucket-cache`. The bucket remains canonical; the local
-`.brainlink/brainlink.db` stays a disposable index. Run `index` after remote
+`.brainlink/index.json` stays a disposable index artifact. Run `index` after remote
 bucket changes before relying on `search`, `context`, graph or validation
 commands. Watch mode is only supported for local filesystem vaults.
 
@@ -301,7 +317,7 @@ vault/
     research-agent/
       source-review-policy.md
   .brainlink/
-    brainlink.db
+    index.json
 ```
 
 Permanent data:
@@ -311,7 +327,7 @@ Permanent data:
 
 Rebuildable data:
 
-- `.brainlink/brainlink.db`
+- `.brainlink/index.json`
 - full-text records
 - local embedding vectors
 - local embedding buckets
@@ -395,6 +411,7 @@ blink agent upgrade
 ```
 
 This configures `~/.codex/config.toml` with Brainlink MCP (`brainlink-mcp`) so Brainlink is available by default in agent sessions.
+`agent install` and `agent upgrade` also apply the MCP `fully-auto` bootstrap policy by default (`enforceBootstrap`, `enforceContextFirst`, `autoBootstrapOnRead`, `autoBootstrapOnStartup` all enabled).
 
 If you are inside this repository and want plugin gallery setup too:
 
@@ -514,8 +531,12 @@ Available tools:
 - `brainlink_recommendations`: return an automatic action plan so agents can run Brainlink in the recommended order.
 - `brainlink_context`: read indexed context for a task or question.
 - `brainlink_search`: search indexed notes.
+- `brainlink_dedupe`: detect duplicate candidates using exact hash + semantic similarity scores.
+- `brainlink_resolve_duplicate`: resolve duplicate pairs (`merge`, `link`, `ignore`) with connectivity-safe fallback edges.
 - `brainlink_add_note`: write durable Markdown memory and reindex.
 - `brainlink_add_file`: ingest a local file as a note and reindex.
+- `brainlink_volatile_add`: write temporary agent-decided memory with TTL; volatile sections are included in context and never create durable graph edges.
+- `brainlink_volatile_clear`: clear temporary memory for the current vault/agent namespace.
 - `brainlink_index`: rebuild the vault index.
 - `brainlink_stats`: read indexed vault statistics.
 - `brainlink_validate`: validate broken links and orphan notes.
@@ -541,7 +562,7 @@ Agents can raise the importance of a relationship by putting priority markers on
 Related: [[Incident Runbook]] #critical
 ```
 
-Indexed edges expose `weight` and `priority` (`low`, `normal`, `high`, `critical`) through CLI JSON, HTTP graph APIs and `brainlink_graph`.
+Indexed edges expose `weight` and `priority` (`low`, `normal`, `high`, `critical`) through CLI JSON, HTTP graph APIs and `brainlink_graph`. Brainlink promotes only representative graph links per note: high-priority and high-weight links win, structural hub links such as `Memory Hub`, `Knowledge Root`, `MOC` and map notes are suppressed when stronger direct links exist, and old indexes are rebuilt automatically when their graph link model version is missing or stale.
 
 ## Graph UI
 
@@ -552,20 +573,40 @@ blink server --host 127.0.0.1 --port 4321 --watch
 ```
 
 By default, the server uses `$HOME/.brainlink/vault`. Pass `--vault ./vault` only when you want to inspect a custom vault.
+By default, `blink server` tries to open the graph in a native desktop GUI window:
+- macOS: Swift + WebKit
+- Windows: PowerShell WinForms WebBrowser
+- Linux: optional Python GTK + WebKit2 (requires `python3` + `gi` + `WebKit2`)
+
+On Linux, native GUI is disabled by default for better startup performance. Enable it with `BRAINLINK_LINUX_NATIVE_GUI=1`.
+If native GUI launch is unavailable on your system, it falls back to dedicated app-window mode and then to the default browser.
+For Chromium-family browsers on Linux (`chromium`, `chromium-browser`, `google-chrome`, `microsoft-edge`, `brave-browser`), Brainlink now auto-applies compatibility flags during launch (`--ozone-platform=x11`, `--ozone-platform-hint=x11`, `--disable-gpu`, `--disable-vulkan`, `--use-gl=swiftshader`, `--disable-features=Vulkan,VaapiVideoDecoder`, `--disable-background-networking`) to avoid common Wayland/Vulkan/VAAPI startup issues.
+On Linux, Brainlink opens the graph through the system default browser first (`xdg-open`), then `$BROWSER`/detected browsers as fallback. Chromium-family app-window mode is optional via `BRAINLINK_LINUX_APP_WINDOW=1`.
+Use `--no-open` to keep it headless.
+When native GUI is used, the GUI window automatically closes when the `blink server` process stops.
 
 The graph UI shows:
 
 - notes as nodes
-- `[[wiki links]]` as weighted edges
+- representative `[[wiki links]]` as weighted edges
 - details opened on node click (tags, outgoing links, backlinks, full Markdown content)
 - neutral graph nodes with segment/group metadata
-- agent selector for isolated views
+- agent selector (id-only labels) for isolated views
 - graph filter matches title, path, tags and note content
+- graph filter keeps hub context nodes visible (`Memory Hub`/`MOC`/high-degree fallback) to preserve relationship readability
 - realtime refresh while `--watch` is enabled
 - graph controls for zoom in, zoom out, fit visible nodes and reset-to-fit-all
-- wheel zoom anchored to cursor position for faster navigation in large graphs
+- wheel zoom (including `cmd+scroll` and `ctrl+scroll`) anchored to cursor position for faster navigation in large graphs
+- continuous target-scale interpolation for wheel/button zoom to avoid abrupt jumps while keeping cursor-anchored focus
+- Bloom-like scene navigation: reset fits the current graph scene, wheel zoom stays anchored to the cursor, and WebGL acceleration draws the dense node and edge layer faster
+- zoom-out floor for large and massive graphs to keep the scene reachable without switching into a separate macro graph mode
+- keyboard shortcuts: `+` zoom in, `-` zoom out, `0` reset fit
+- double-click on canvas zooms in at cursor position
 - floating graph totals (notes, links, tags) below the Brainlink title
-- large-graph rendering safeguards (edge draw caps, lower redraw rate, zoom-aware interaction)
+- graph rendering safeguards (batched canvas drawing across graph sizes, edge draw caps, lower redraw rate, zoom-aware interaction)
+- adaptive CPU safeguards for large graphs: idle frame pacing, throttled background physics updates and cached viewport dimensions to reduce redraw/layout overhead while preserving interaction responsiveness
+- WebGL node and edge acceleration when supported, falling back to Canvas 2D without changing graph behavior
+- large graph LOD keeps a recursive graph-of-graphs model: zoom-out fills the projected macro level toward 1000 lightweight group nodes with sparse strongest-link edges, zoom-in fits the framed node's full child-graph circumference with extra margin before expanding, groups with child groups open another graph level instead of jumping to leaf notes, and zoom-out restores sibling groups
 
 The server indexes before starting by default. Use `--no-index` to skip that step:
 
@@ -584,6 +625,7 @@ Routes:
 - `GET /api/agents`
 - `GET /api/graph`
 - `GET /api/graph-layout`
+- `GET /api/graph-view?x=<x>&y=<y>&w=<width>&h=<height>&scale=<scale>`
 - `GET /api/graph-node?id=<node-id>`
 - `GET /api/search?q=<query>&limit=10&mode=hybrid`
 - `GET /api/context?q=<query>&limit=12&tokens=2000&mode=hybrid`
@@ -667,6 +709,18 @@ blink migrate-vault --from ~/.brainlink/vault --to ./team-vault --report ./migra
 Runs explicit markdown migration between vaults while preserving conflicts as `.conflict-<timestamp>` files.  
 Use `--dry-run` to preview `copied`, `conflicted` and `unchanged` counts before writing.
 
+### `db-import`
+
+```bash
+blink db-import --vault ./team-vault
+blink db-import --vault ./team-vault --db ./legacy/brainlink.db
+blink db-import --vault ./team-vault --db ./legacy/brainlink.db --table legacy_notes --dry-run
+```
+
+Imports durable memory from a legacy SQLite database into Markdown notes (`agents/<agent-id>/*.md`) and reindexes by default.
+When `--db` is omitted, Brainlink auto-detects common legacy paths such as `<vault>/.brainlink/brainlink.db`.
+Use `--agent <id>` to force all imported rows into one namespace, `--limit` for incremental imports, `--dry-run` to preview without writing files, and `--no-index` to defer reindexing.
+
 ### `init`
 
 ```bash
@@ -691,6 +745,28 @@ blink add "Note Title" --vault ./vault --content-file ./notes.md --no-auto-index
 
 Creates a Markdown note under `agents/<agent-id>/`. Common secret patterns are blocked by default; use `--allow-sensitive` only for an intentionally protected vault.
 To avoid disconnected memory, Brainlink auto-adds a fallback wiki edge when a note is written without links, creating agent hub notes when needed.
+`add` also returns `possibleDuplicates` (exact hash + semantic candidates) so agents can resolve duplicate memory right after writes.
+
+### `dedupe`
+
+```bash
+blink dedupe --vault ./vault --json
+blink dedupe --vault ./vault --agent coding-agent --limit 20 --min-score 0.92 --json
+blink dedupe --vault ./vault --no-semantic --json
+```
+
+Detects `possibleDuplicate` pairs using exact content hashes and optional semantic similarity.
+
+### `dedupe-resolve`
+
+```bash
+blink dedupe-resolve --vault ./vault --left agents/shared/a.md --right agents/shared/b.md --action merge --json
+blink dedupe-resolve --vault ./vault --left agents/shared/a.md --right agents/shared/b.md --action link --json
+blink dedupe-resolve --vault ./vault --left agents/shared/a.md --right agents/shared/b.md --action ignore --json
+```
+
+Resolves a duplicate pair with `merge`, `link` or `ignore`.
+When action is not `merge`, Brainlink still creates a low-priority related edge (`#related-to`) so notes remain connected.
 
 ### `index`
 
@@ -701,6 +777,38 @@ blink index --vault ./vault
 
 Rebuilds the local index from Markdown files.
 
+### `bench`
+
+```bash
+blink bench --vault ./vault
+blink bench --vault ./vault --watch
+blink bench --vault ./vault --watch --debounce 500
+blink bench --vault ./vault --json
+```
+
+Runs indexing with realtime phase telemetry (`start`, `scan`, `parse`, `embed`, `persist`, `packs`, `complete`) and prints a benchmark summary at the end of each run.
+
+Summary includes compression behavior for `.blpk` packs when rebuild happens:
+- pack rebuild reason
+- pack count and pack build duration
+- uncompressed input bytes vs compressed output bytes
+- saved percentage
+- objective guardrails (minimum savings and maximum latency regression thresholds)
+
+Use `--watch` to keep benchmarking incremental reindex runs after Markdown changes (local filesystem vaults only).
+When `.brainlink/search-packs/manifest.json` is missing but `.blpk` files exist, Brainlink repairs the manifest first and avoids unnecessary full pack rebuild on small edits.
+
+### `pack-backup`
+
+```bash
+blink pack-backup --vault ./vault
+blink pack-backup --vault ./vault --output ./vault/.brainlink/backups/custom.blpkbak.gz
+blink pack-backup --vault ./vault --json
+```
+
+Creates an offline backup artifact of encrypted search packs with a second compression pass.
+This is intentionally outside the online retrieval path (`index`, `search`, `context`).
+
 ### `agents`
 
 ```bash
@@ -723,11 +831,12 @@ If `--mode` or `--limit` is omitted, Brainlink resolves values from the current
 
 Modes:
 
-- `hybrid`: default; combines SQLite FTS with local embedding similarity.
-- `fts`: exact lexical retrieval through SQLite FTS.
+- `hybrid`: default; combines lexical matching with local embedding similarity.
+- `fts`: exact lexical retrieval from the file index.
 - `semantic`: local deterministic embedding similarity only.
 
 Hybrid results are cached in-memory for a short TTL and invalidated automatically when the local index file changes.
+Context selection uses a middle-out strategy: it starts from the strongest chunk in a note and expands to neighboring chunks while respecting token budget.
 
 ### `context`
 
@@ -738,6 +847,7 @@ blink context "question" --vault ./vault --agent coding-agent --mode hybrid --js
 ```
 
 Builds a compact context package for an agent.
+Repeated calls with the same vault, agent, query, mode and token/limit settings are served from a short in-memory cache while the index is unchanged.
 
 ### `links`
 
@@ -822,9 +932,15 @@ Watches Markdown files and rebuilds the index when notes change.
 ```bash
 blink server --watch
 blink server --vault ./vault --watch
+blink server --vault ./vault --watch --no-open
 ```
 
 Starts the local read-only graph UI and HTTP API.
+By default, it tries to open a native desktop GUI window for the graph URL.
+On Linux, native GUI is disabled by default; enable it with `BRAINLINK_LINUX_NATIVE_GUI=1`.
+If native GUI launch is unavailable, it falls back to dedicated app-window mode and then browser open.
+When fallback opens Chromium-family browsers on Linux, Brainlink automatically uses compatibility launch flags for stable rendering on Ubuntu/Wayland setups.
+Use `--no-open` to skip that behavior.
 
 The HTTP server only binds to loopback hosts such as `127.0.0.1`, `localhost` or `::1`.
 
@@ -865,6 +981,13 @@ If no `vault` is configured and no `--vault` flag is passed, Brainlink uses `$HO
   "embeddingProvider": "local",
   "defaultSearchMode": "hybrid",
   "chunkSize": 1200,
+  "searchPack": {
+    "rowChunkSize": 5000,
+    "compressionLevel": 5,
+    "useDictionary": true,
+    "guardrailMinSavingsPercent": 8,
+    "guardrailMaxLatencyRegressionPercent": 5
+  },
   "agentProfiles": {
     "coding-agent": {
       "defaultSearchMode": "semantic",
@@ -976,7 +1099,7 @@ src/
   application/      use cases
   cli/              command-line adapter
   domain/           pure knowledge rules
-  infrastructure/   filesystem and SQLite adapters
+  infrastructure/   filesystem and index adapters
 ```
 
 Detailed notes:
@@ -988,7 +1111,6 @@ Detailed notes:
 ## Current Limits
 
 - Semantic search uses deterministic local embeddings, not a remote model provider.
-- Semantic search uses SQLite embedding buckets to narrow candidates before cosine scoring.
 - `embeddingProvider` currently supports `local` and `none`.
 - Link resolution is title-based inside each agent namespace, with `shared` as fallback.
 - HTTP API is local and unauthenticated.
@@ -999,7 +1121,7 @@ Detailed notes:
 The `0.1.0-beta` line is intended to stabilize the local-first memory loop:
 
 - Markdown as durable memory.
-- SQLite FTS plus local embeddings and semantic buckets as rebuildable retrieval index.
+- Rebuildable file index plus local embeddings and encrypted pack exports.
 - CLI as the primary agent interface.
 - HTTP graph API and frontend as inspection tools.
 - Agent namespaces to avoid context mixing.
@@ -1015,7 +1137,7 @@ Brainlink is local-first by default.
 - Brainlink HTTP is localhost-only and refuses non-loopback hosts.
 - Brainlink blocks common secret patterns by default when adding notes. Use `--allow-sensitive` only for intentional, protected vaults.
 - Do not store secrets, credentials, API keys or regulated personal data unless the vault is protected by your own storage controls.
-- Treat `.brainlink/brainlink.db` as disposable derived data.
+- Treat `.brainlink/index.json` and `.brainlink/search-packs/` as disposable derived artifacts.
 
 See [SECURITY.md](SECURITY.md).
 
@@ -1026,6 +1148,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md).
 ## License
 
 MIT. See [LICENSE](LICENSE).
+Copyright (c) 2026 Substructa. See [COPYRIGHT.md](COPYRIGHT.md).
 
 ### Memory Optimization Loop (1-7)
 

package/SECURITY.md

@@ -7,7 +7,7 @@ Brainlink is local-first.
 - The HTTP server binds to `127.0.0.1` by default.
 - The HTTP server always refuses non-loopback hosts.
 - The HTTP server is read-only and does not expose note creation, indexing or update routes.
-- The SQLite database is a derived local index.
+- Local index artifacts (`.brainlink/index.json` and `.brainlink/search-packs/`) are derived data.
 - Markdown files are user-owned source data.
 - Brainlink-created Markdown files use `0600` permissions.
 - Brainlink-created directories and `.brainlink` use `0700` permissions.

package/dist/application/analyze-vault.js

@@ -1,7 +1,5 @@
 import { stat } from 'node:fs/promises';
-import { existsSync, readdirSync } from 'node:fs';
 import { performance } from 'node:perf_hooks';
-import { join } from 'node:path';
 import { validateGraph, getBrokenLinks, getOrphanNodes, getVaultStats } from '../domain/graph-analysis.js';
 import { ensureVault, listVaultFiles, readMarkdownFiles } from '../infrastructure/file-system-vault.js';
 import { resolveAgentRuntimeDefaults } from '../infrastructure/config.js';
@@ -96,23 +94,11 @@ export const doctorVault = async (vaultPath) => {
     const files = await readMarkdownFiles(absoluteVaultPath);
     const graph = await getGraphSummary(absoluteVaultPath);
     const validation = validateGraph(graph);
-    const backupPath = join(absoluteVaultPath, '.brainlink', 'brainlink.db.backup');
-    const snapshotDirectory = join(absoluteVaultPath, '.brainlink', 'brainlink.db.backup.snapshots');
-    const hasBackup = existsSync(backupPath);
-    const snapshotCount = existsSync(snapshotDirectory)
-        ? readdirSync(snapshotDirectory).filter((name) => name.endsWith('.db')).length
-        : 0;
-    const backupReady = graph.nodes.length === 0 || hasBackup;
     const checks = [
         createCheck('vault', true, `Vault ready at ${absoluteVaultPath}`),
         createCheck('markdown-files', files.length > 0, `${files.length} markdown files found`),
         createCheck('index', graph.nodes.length > 0, `${graph.nodes.length} indexed documents found`),
-        createCheck('broken-links', validation.brokenLinks.length === 0, `${validation.brokenLinks.length} broken links found`),
-        createCheck('index-backup', backupReady, backupReady
-            ? (hasBackup
-                ? `SQLite recovery snapshot is available (${snapshotCount} rotating snapshots)`
-                : 'No index yet. Snapshot will be created after first indexing run')
-            : 'Recovery snapshot missing. Run blink index to create a rollback snapshot')
+        createCheck('broken-links', validation.brokenLinks.length === 0, `${validation.brokenLinks.length} broken links found`)
     ];
     const recommendations = files.length === 0 && graph.nodes.length === 0
         ? [

package/dist/application/build-context.js

@@ -1,13 +1,74 @@
+import { stat } from 'node:fs/promises';
 import { formatContextPackage, selectContextSections } from '../domain/context.js';
+import { indexStoragePath } from '../infrastructure/file-index.js';
+import { searchVolatileMemory, volatileMemoryStoragePath } from '../infrastructure/volatile-memory.js';
 import { searchKnowledge } from './search-knowledge.js';
+const contextCacheTtlMs = 45_000;
+const contextCacheMaxEntries = 200;
+const contextCache = new Map();
+const readFileSignature = async (path) => {
+    try {
+        const info = await stat(path);
+        return `${Math.floor(info.mtimeMs)}:${info.size}`;
+    }
+    catch {
+        return '0:0';
+    }
+};
+const readContextDataSignature = async (vaultPath) => `${await readFileSignature(indexStoragePath(vaultPath))}|${await readFileSignature(volatileMemoryStoragePath(vaultPath))}`;
+const toCacheKey = (vaultPath, query, limit, maxTokens, agentId, mode) => JSON.stringify({
+    vaultPath,
+    query: query.trim().toLowerCase(),
+    limit,
+    maxTokens,
+    agentId: agentId?.trim().toLowerCase() ?? '*',
+    mode: mode ?? 'default'
+});
+const contextCacheGet = (key, dataSignature) => {
+    const entry = contextCache.get(key);
+    if (!entry) {
+        return undefined;
+    }
+    const fresh = Date.now() - entry.createdAt <= contextCacheTtlMs && entry.dataSignature === dataSignature;
+    if (!fresh) {
+        contextCache.delete(key);
+        return undefined;
+    }
+    return entry.context;
+};
+const contextCacheSet = (entry) => {
+    contextCache.set(entry.key, entry);
+    if (contextCache.size <= contextCacheMaxEntries) {
+        return;
+    }
+    const overflow = contextCache.size - contextCacheMaxEntries;
+    const keys = Array.from(contextCache.keys()).slice(0, overflow);
+    keys.forEach((key) => contextCache.delete(key));
+};
 export const buildContextPackage = async (vaultPath, query, limit, maxTokens, agentId, mode) => {
+    const cacheKey = toCacheKey(vaultPath, query, limit, maxTokens, agentId, mode);
+    const dataSignature = await readContextDataSignature(vaultPath);
+    const cached = contextCacheGet(cacheKey, dataSignature);
+    if (cached) {
+        return cached;
+    }
     const results = await searchKnowledge(vaultPath, query, limit, agentId, mode);
-    const sections = selectContextSections(results, maxTokens);
-    return {
+    const durableSections = selectContextSections(results, maxTokens);
+    const volatileSections = await searchVolatileMemory(vaultPath, query, Math.min(3, limit), agentId, mode ?? 'hybrid');
+    const sections = [...volatileSections, ...durableSections];
+    const context = {
         query,
         sections,
-        content: formatContextPackage(query, sections)
+        content: formatContextPackage(query, sections),
+        ...(volatileSections.length > 0 ? { volatileSections } : {})
     };
+    contextCacheSet({
+        key: cacheKey,
+        createdAt: Date.now(),
+        dataSignature,
+        context
+    });
+    return context;
 };
 export const buildContext = async (vaultPath, query, limit, maxTokens, agentId, mode) => {
     const contextPackage = await buildContextPackage(vaultPath, query, limit, maxTokens, agentId, mode);