@abhishekmcp/notes 0.2.0 → 0.3.0

package/README.md

@@ -1,40 +1,82 @@
 # @abhishekmcp/notes
 
-An [MCP](https://modelcontextprotocol.io) server for managing local markdown notes. Lets any MCP client (Claude Desktop, Claude Code, Cursor, …) search, read, create, link, and organize notes in a folder on your machine.
+An [MCP](https://modelcontextprotocol.io) server for managing local markdown notes. Lets any MCP client (Claude Desktop, Claude Code, Cursor, …) search, link, and organize the notes in a folder on your machine — with ranked full-text search, tags, todos, and a wiki-link knowledge graph.
+
+Pure JavaScript, no native dependencies, no API keys — everything runs locally.
 
 ## Features
 
-**Tools**
-- `list_notes` — list all notes, newest first
-- `read_note` — read a note's contents
-- `create_note` — create a new note (optional overwrite)
-- `append_note` — append to a note (great for journals/logs)
+### Notes (token-efficient I/O)
+- `list_notes` — list notes (newest first) with pagination (`offset`/`limit`) and an optional `tag` filter
+- `read_note` — read a note; optionally just one heading's `section`, or a character window (`offset`/`limit`) with a truncation flag
+- `get_outline` — return only a note's heading tree (grasp a big note in a few tokens)
+- `create_note` — create a new note (optional `overwrite`)
+- `append_note` — append to a note, creating it if missing (great for journals/logs)
 - `delete_note` — delete a note
-- `search_notes` — full-text search across all notes
-- `get_backlinks` — find notes linking to a note via `[[wiki-link]]` syntax
-
-**Resources**
+- `move_note` — rename/move a note **and rewrite every `[[wiki-link]]`** across the vault that points at it
+
+### Search & discovery
+- `search_notes` — ranked full-text search ([MiniSearch](https://github.com/lucaong/minisearch)); supports `fuzzy` and `prefix` matching, a `field` filter (`title`/`tag`/`body`/`path`), and returns ranked snippets with surrounding context
+- `semantic_search` — **meaning-based** search using local embeddings; finds related notes even with no shared keywords (e.g. "puppy" matches a note about "canine companions"). Optional `hybrid` mode fuses semantic + keyword ranking
+- `list_tags` — every tag across the vault with note counts
+- `list_todos` — aggregate `- [ ]` / `- [x]` checkboxes across all notes
+
+### Knowledge graph
+- `get_backlinks` — notes linking to a note via `[[wiki-link]]` syntax
+- `get_neighbors` — notes within N hops over the (undirected) link graph (depth/limit capped)
+- `find_path` — shortest wiki-link chain between two notes
+- `related_notes` — notes ranked by shared links + shared tags
+- `graph_overview` — aggregate health: note/link/tag counts, top hubs, orphans, broken-link count
+- `broken_links` — wiki-links that point at notes which don't exist
+
+### Resources
 - Every note is exposed as a `notes://<name>` resource.
 
-All file access is sandboxed to the notes directory — paths that try to escape it are rejected.
+### Frontmatter & tags
+Notes may start with a YAML frontmatter block; `title` and `tags` (a list or comma-separated string) are recognized. Inline `#hashtags` in the body are also collected as tags.
 
-## Install & build
-
-```bash
-npm install
-npm run build
+```markdown
+---
+title: My Note
+tags: [project, ideas]
+---
+# My Note
+Links to [[another-note]]. Some inline #tag too.
 ```
 
 ## Configuration
 
-Set `NOTES_DIR` to choose where notes live (defaults to `~/notes`):
+All via environment variables:
+
+| Variable | Default | Effect |
+|----------|---------|--------|
+| `NOTES_DIR` | `~/notes` | Directory where notes live (a leading `~` is expanded). |
+| `NOTES_READONLY` | _unset_ | Set to `1` to disable all mutating tools (`create`/`append`/`delete`/`move` are not even registered) — safe for sharing a vault. |
+| `NOTES_NO_CACHE` | _unset_ | Set to `1` to skip the on-disk index cache and rebuild in memory each start. |
+| `NOTES_MODEL_DIR` | `~/.cache/mcp-notes/models` | Where the semantic-search embedding model is cached. |
+
+### Semantic search & the embedding model
+`semantic_search` runs the [all-MiniLM-L6-v2](https://huggingface.co/Xenova/all-MiniLM-L6-v2) model **locally** via WebAssembly ([onnxruntime-web](https://github.com/microsoft/onnxruntime)) — no API keys, no native dependencies, no data leaves your machine. The quantized model (~23 MB) is downloaded **once** on first use into `NOTES_MODEL_DIR` and cached; embeddings are stored in `<NOTES_DIR>/.notes-embeddings.json` and incrementally updated as notes change. The first `semantic_search` call needs network access for the download and embeds the whole vault; everything after that is offline and fast. Keyword search and all other tools work without ever triggering this.
+
+### Index cache
+For fast warm starts the server persists its search index to `<NOTES_DIR>/.notes-index.json` and, on startup, incrementally re-parses only the notes that changed (by mtime/size) since last run. The cache is rebuilt automatically if it's missing, unreadable, or from an older index version. Files on disk are always the source of truth.
+
+## Security
+
+All filesystem access is sandboxed to the notes directory:
+- Path traversal (`../`) and absolute paths are rejected.
+- Symlinks inside the vault that resolve outside it are rejected (realpath containment).
+- Single files above a size limit are refused (DoS / context guard).
+- Writes are atomic (temp file + rename), so a crash can't leave a torn note.
+
+## Usage
+
+### Claude Code
 
 ```bash
-export NOTES_DIR="$HOME/my-notes"
+claude mcp add notes --env NOTES_DIR=$HOME/notes -- npx -y @abhishekmcp/notes
 ```
 
-## Connecting to a client
-
 ### Claude Desktop
 
 Add to `claude_desktop_config.json`:
@@ -43,38 +85,27 @@ Add to `claude_desktop_config.json`:
 {
   "mcpServers": {
     "notes": {
-      "command": "node",
-      "args": ["/absolute/path/to/mcp-suite/servers/notes/dist/index.js"],
+      "command": "npx",
+      "args": ["-y", "@abhishekmcp/notes"],
       "env": { "NOTES_DIR": "/absolute/path/to/your/notes" }
     }
   }
 }
 ```
 
-### Claude Code
+To share a vault read-only, add `"NOTES_READONLY": "1"` to `env`.
+
+## Develop from source
 
 ```bash
-claude mcp add notes --env NOTES_DIR=$HOME/notes -- node /absolute/path/to/mcp-suite/servers/notes/dist/index.js
+npm install                      # from the repo root
+npm run build -w servers/notes
+node servers/notes/dist/index.js # NOTES_DIR=... to point at a vault
 ```
 
 ## Publishing to npm
 
-This package publishes automatically via GitHub Actions (Trusted Publishing / OIDC) when a
-release tagged `notes-v<version>` is created. See the repo root for the CD workflow.
-
-Once published, users can run it without cloning:
-
-```json
-{
-  "mcpServers": {
-    "notes": {
-      "command": "npx",
-      "args": ["-y", "@abhishekmcp/notes"],
-      "env": { "NOTES_DIR": "/path/to/notes" }
-    }
-  }
-}
-```
+Publishes automatically via GitHub Actions (Trusted Publishing / OIDC) when a release tagged `notes-v<version>` is created. See the repo root for the CD workflow.
 
 ## License
 

package/dist/config.d.ts

@@ -15,3 +15,27 @@ export declare function getIndexPath(): string;
 export declare function isReadOnly(): boolean;
 /** When true, skip the on-disk index cache and rebuild in memory each start. */
 export declare function cacheDisabled(): boolean;
+/** Embedding model identity (recorded in the cache to invalidate on change). */
+export declare const EMBED_MODEL_ID = "Xenova/all-MiniLM-L6-v2:quantized";
+/** Embedding dimensionality of all-MiniLM-L6-v2. */
+export declare const EMBED_DIM = 384;
+/** Max WordPiece tokens fed to the model (longer notes are truncated). */
+export declare const EMBED_MAX_TOKENS = 256;
+/** Bump to force re-embedding of every note on upgrade. */
+export declare const EMBED_CACHE_VERSION = 1;
+/** Sidecar cache of per-note vectors, kept inside the notes dir. */
+export declare const EMBEDDINGS_FILENAME = ".notes-embeddings.json";
+/** Quantized ONNX model (~23 MB) — downloaded once at runtime. */
+export declare const EMBED_MODEL_URL = "https://huggingface.co/Xenova/all-MiniLM-L6-v2/resolve/main/onnx/model_quantized.onnx";
+/** BERT-uncased vocabulary (~232 KB) for the hand-rolled tokenizer. */
+export declare const EMBED_VOCAB_URL = "https://huggingface.co/Xenova/all-MiniLM-L6-v2/resolve/main/vocab.txt";
+/** Local filenames for the cached artifacts. */
+export declare const EMBED_MODEL_FILE = "all-MiniLM-L6-v2.quantized.onnx";
+export declare const EMBED_VOCAB_FILE = "all-MiniLM-L6-v2.vocab.txt";
+/**
+ * Directory where the embedding model + vocab are cached (downloaded once per
+ * machine). Override with NOTES_MODEL_DIR; defaults to ~/.cache/mcp-notes/models.
+ */
+export declare function getModelDir(): string;
+/** Absolute path to the persisted embeddings cache (sidecar to the text index). */
+export declare function getEmbeddingsPath(): string;

package/dist/config.js

@@ -29,4 +29,39 @@ export function isReadOnly() {
 export function cacheDisabled() {
     return process.env.NOTES_NO_CACHE === "1";
 }
+// --- Semantic search (v0.3) ----------------------------------------------
+/** Embedding model identity (recorded in the cache to invalidate on change). */
+export const EMBED_MODEL_ID = "Xenova/all-MiniLM-L6-v2:quantized";
+/** Embedding dimensionality of all-MiniLM-L6-v2. */
+export const EMBED_DIM = 384;
+/** Max WordPiece tokens fed to the model (longer notes are truncated). */
+export const EMBED_MAX_TOKENS = 256;
+/** Bump to force re-embedding of every note on upgrade. */
+export const EMBED_CACHE_VERSION = 1;
+/** Sidecar cache of per-note vectors, kept inside the notes dir. */
+export const EMBEDDINGS_FILENAME = ".notes-embeddings.json";
+const HF_BASE = "https://huggingface.co/Xenova/all-MiniLM-L6-v2/resolve/main";
+/** Quantized ONNX model (~23 MB) — downloaded once at runtime. */
+export const EMBED_MODEL_URL = `${HF_BASE}/onnx/model_quantized.onnx`;
+/** BERT-uncased vocabulary (~232 KB) for the hand-rolled tokenizer. */
+export const EMBED_VOCAB_URL = `${HF_BASE}/vocab.txt`;
+/** Local filenames for the cached artifacts. */
+export const EMBED_MODEL_FILE = "all-MiniLM-L6-v2.quantized.onnx";
+export const EMBED_VOCAB_FILE = "all-MiniLM-L6-v2.vocab.txt";
+/**
+ * Directory where the embedding model + vocab are cached (downloaded once per
+ * machine). Override with NOTES_MODEL_DIR; defaults to ~/.cache/mcp-notes/models.
+ */
+export function getModelDir() {
+    const override = process.env.NOTES_MODEL_DIR;
+    if (override) {
+        const expanded = override.startsWith("~") ? path.join(homedir(), override.slice(1)) : override;
+        return path.resolve(expanded);
+    }
+    return path.join(homedir(), ".cache", "mcp-notes", "models");
+}
+/** Absolute path to the persisted embeddings cache (sidecar to the text index). */
+export function getEmbeddingsPath() {
+    return path.join(getNotesDir(), EMBEDDINGS_FILENAME);
+}
 //# sourceMappingURL=config.js.map

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package/dist/embed.d.ts

@@ -0,0 +1,9 @@
+/** Idempotent, concurrency-safe lazy initialization. */
+export declare function ensureModel(): Promise<void>;
+/** True once the model has been downloaded + loaded. */
+export declare function isReady(): boolean;
+/**
+ * Embed a single text into an L2-normalized 384-dim vector (cosine == dot
+ * product). Mean-pools the model's last_hidden_state over the attention mask.
+ */
+export declare function embed(text: string): Promise<Float32Array>;

package/dist/embed.js

@@ -0,0 +1,134 @@
+/**
+ * Lazy embedding engine: runs all-MiniLM-L6-v2 (ONNX) on onnxruntime-web (WASM,
+ * no native deps). The model + vocab are downloaded once to a persistent cache
+ * on first use; nothing here runs at server startup. `onnxruntime-web` is
+ * dynamically imported so a server that never does semantic search never loads
+ * the WASM runtime.
+ */
+import { promises as fs } from "node:fs";
+import { createRequire } from "node:module";
+import path from "node:path";
+import { EMBED_DIM, EMBED_MAX_TOKENS, EMBED_MODEL_FILE, EMBED_MODEL_URL, EMBED_VOCAB_FILE, EMBED_VOCAB_URL, getModelDir, } from "./config.js";
+import { WordPieceTokenizer } from "./tokenizer.js";
+let session = null;
+let tokenizer = null;
+let initPromise = null;
+/** Download a URL to `dest` atomically (temp + rename), retrying on 429/5xx. */
+async function download(url, dest) {
+    let lastErr;
+    for (let attempt = 0; attempt < 4; attempt++) {
+        try {
+            const res = await fetch(url);
+            if (res.status === 429 || res.status >= 500) {
+                throw new Error(`HTTP ${res.status} fetching ${url}`);
+            }
+            if (!res.ok)
+                throw new Error(`HTTP ${res.status} fetching ${url}`);
+            const buf = Buffer.from(await res.arrayBuffer());
+            const tmp = `${dest}.${process.pid}.tmp`;
+            await fs.writeFile(tmp, buf);
+            await fs.rename(tmp, dest);
+            return;
+        }
+        catch (err) {
+            lastErr = err;
+            await new Promise((r) => setTimeout(r, 500 * 2 ** attempt)); // backoff
+        }
+    }
+    throw new Error(`Failed to download ${url}: ${lastErr?.message ?? lastErr}`);
+}
+/** Ensure a cached file exists, downloading it if missing. */
+async function ensureFile(url, dest) {
+    try {
+        await fs.access(dest);
+    }
+    catch {
+        await fs.mkdir(path.dirname(dest), { recursive: true });
+        await download(url, dest);
+    }
+}
+/** Download artifacts (once) and build the tokenizer + WASM inference session. */
+async function init() {
+    const dir = getModelDir();
+    const modelPath = path.join(dir, EMBED_MODEL_FILE);
+    const vocabPath = path.join(dir, EMBED_VOCAB_FILE);
+    await ensureFile(EMBED_VOCAB_URL, vocabPath);
+    await ensureFile(EMBED_MODEL_URL, modelPath);
+    tokenizer = new WordPieceTokenizer(await fs.readFile(vocabPath, "utf8"));
+    const ort = await import("onnxruntime-web");
+    ort.env.wasm.numThreads = 1; // single-thread: no SharedArrayBuffer / worker isolation needed
+    // Best-effort: point the WASM loader at the .wasm shipped in node_modules.
+    // (onnxruntime-web self-resolves from its own module URL when this isn't set.)
+    try {
+        const require = createRequire(import.meta.url);
+        ort.env.wasm.wasmPaths = path.dirname(require.resolve("onnxruntime-web")) + path.sep;
+    }
+    catch {
+        /* fall back to onnxruntime-web's own resolution */
+    }
+    const modelBytes = new Uint8Array(await fs.readFile(modelPath));
+    session = await ort.InferenceSession.create(modelBytes, { executionProviders: ["wasm"] });
+}
+/** Idempotent, concurrency-safe lazy initialization. */
+export async function ensureModel() {
+    if (session && tokenizer)
+        return;
+    if (!initPromise) {
+        initPromise = init().catch((err) => {
+            initPromise = null; // allow retry on a later call
+            throw err;
+        });
+    }
+    await initPromise;
+}
+/** True once the model has been downloaded + loaded. */
+export function isReady() {
+    return session !== null && tokenizer !== null;
+}
+/**
+ * Embed a single text into an L2-normalized 384-dim vector (cosine == dot
+ * product). Mean-pools the model's last_hidden_state over the attention mask.
+ */
+export async function embed(text) {
+    await ensureModel();
+    const ort = await import("onnxruntime-web");
+    const tok = tokenizer.encode(text, EMBED_MAX_TOKENS);
+    const seq = tok.inputIds.length;
+    const dims = [1, seq];
+    const feeds = {
+        input_ids: new ort.Tensor("int64", BigInt64Array.from(tok.inputIds, BigInt), dims),
+        attention_mask: new ort.Tensor("int64", BigInt64Array.from(tok.attentionMask, BigInt), dims),
+    };
+    // Some exports require token_type_ids (all-zero for a single segment).
+    if (session.inputNames.includes("token_type_ids")) {
+        feeds.token_type_ids = new ort.Tensor("int64", new BigInt64Array(seq), dims);
+    }
+    const results = await session.run(feeds);
+    const outName = session.outputNames.includes("last_hidden_state")
+        ? "last_hidden_state"
+        : session.outputNames[0];
+    const data = results[outName].data; // [1, seq, EMBED_DIM]
+    // Mean-pool over tokens weighted by the attention mask, then L2-normalize.
+    const out = new Float32Array(EMBED_DIM);
+    let maskSum = 0;
+    for (let t = 0; t < seq; t++) {
+        const m = tok.attentionMask[t];
+        if (!m)
+            continue;
+        maskSum += m;
+        const base = t * EMBED_DIM;
+        for (let d = 0; d < EMBED_DIM; d++)
+            out[d] += data[base + d] * m;
+    }
+    const denom = maskSum || 1;
+    let norm = 0;
+    for (let d = 0; d < EMBED_DIM; d++) {
+        out[d] /= denom;
+        norm += out[d] * out[d];
+    }
+    norm = Math.sqrt(norm) || 1;
+    for (let d = 0; d < EMBED_DIM; d++)
+        out[d] /= norm;
+    return out;
+}
+//# sourceMappingURL=embed.js.map

package/dist/embed.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"embed.js","sourceRoot":"","sources":["../src/embed.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AACH,OAAO,EAAE,QAAQ,IAAI,EAAE,EAAE,MAAM,SAAS,CAAC;AACzC,OAAO,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAC5C,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B,OAAO,EACL,SAAS,EACT,gBAAgB,EAChB,gBAAgB,EAChB,eAAe,EACf,gBAAgB,EAChB,eAAe,EACf,WAAW,GACZ,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,kBAAkB,EAAE,MAAM,gBAAgB,CAAC;AAEpD,IAAI,OAAO,GAAkC,IAAI,CAAC;AAClD,IAAI,SAAS,GAA8B,IAAI,CAAC;AAChD,IAAI,WAAW,GAAyB,IAAI,CAAC;AAE7C,gFAAgF;AAChF,KAAK,UAAU,QAAQ,CAAC,GAAW,EAAE,IAAY;IAC/C,IAAI,OAAgB,CAAC;IACrB,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,CAAC,EAAE,OAAO,EAAE,EAAE,CAAC;QAC7C,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;YAC7B,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,EAAE,CAAC,CAAC;YACxD,CAAC;YACD,IAAI,CAAC,GAAG,CAAC,EAAE;gBAAE,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,EAAE,CAAC,CAAC;YACnE,MAAM,GAAG,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAC;YACjD,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,OAAO,CAAC,GAAG,MAAM,CAAC;YACzC,MAAM,EAAE,CAAC,SAAS,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;YAC7B,MAAM,EAAE,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;YAC3B,OAAO;QACT,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,OAAO,GAAG,GAAG,CAAC;YACd,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,GAAG,GAAG,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,UAAU;QACzE,CAAC;IACH,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,sBAAsB,GAAG,KAAM,OAAiB,EAAE,OAAO,IAAI,OAAO,EAAE,CAAC,CAAC;AAC1F,CAAC;AAED,8DAA8D;AAC9D,KAAK,UAAU,UAAU,CAAC,GAAW,EAAE,IAAY;IACjD,IAAI,CAAC;QACH,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IACxB,CAAC;IAAC,MAAM,CAAC;QACP,MAAM,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACxD,MAAM,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;IAC5B,CAAC;AACH,CAAC;AAED,kFAAkF;AAClF,KAAK,UAAU,IAAI;IACjB,MAAM,GAAG,GAAG,WAAW,EAAE,CAAC;IAC1B,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAC;IACnD,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAC;IACnD,MAAM,UAAU,CAAC,eAAe,EAAE,SAAS,CAAC,CAAC;IAC7C,MAAM,UAAU,CAAC,eAAe,EAAE,SAAS,CAAC,CAAC;IAE7C,SAAS,GAAG,IAAI,kBAAkB,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC,CAAC;IAEzE,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,iBAAiB,CAAC,CAAC;IAC5C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,gEAAgE;IAC7F,2EAA2E;IAC3E,+EAA+E;IAC/E,IAAI,CAAC;QACH,MAAM,OAAO,GAAG,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC/C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC;IACvF,CAAC;IAAC,MAAM,CAAC;QACP,mDAAmD;IACrD,CAAC;IAED,MAAM,UAAU,GAAG,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC;IAChE,OAAO,GAAG,MAAM,GAAG,CAAC,gBAAgB,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,kBAAkB,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;AAC5F,CAAC;AAED,wDAAwD;AACxD,MAAM,CAAC,KAAK,UAAU,WAAW;IAC/B,IAAI,OAAO,IAAI,SAAS;QAAE,OAAO;IACjC,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,WAAW,GAAG,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,EAAE;YACjC,WAAW,GAAG,IAAI,CAAC,CAAC,8BAA8B;YAClD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;IACL,CAAC;IACD,MAAM,WAAW,CAAC;AACpB,CAAC;AAED,wDAAwD;AACxD,MAAM,UAAU,OAAO;IACrB,OAAO,OAAO,KAAK,IAAI,IAAI,SAAS,KAAK,IAAI,CAAC;AAChD,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,KAAK,CAAC,IAAY;IACtC,MAAM,WAAW,EAAE,CAAC;IACpB,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,iBAAiB,CAAC,CAAC;IAC5C,MAAM,GAAG,GAAG,SAAU,CAAC,MAAM,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAC;IACtD,MAAM,GAAG,GAAG,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC;IAEtB,MAAM,KAAK,GAAiC;QAC1C,SAAS,EAAE,IAAI,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,EAAE,IAAI,CAAC;QAClF,cAAc,EAAE,IAAI,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,aAAa,EAAE,MAAM,CAAC,EAAE,IAAI,CAAC;KAC7F,CAAC;IACF,uEAAuE;IACvE,IAAI,OAAQ,CAAC,UAAU,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;QACnD,KAAK,CAAC,cAAc,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,IAAI,aAAa,CAAC,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC;IAC/E,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,OAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;IAC1C,MAAM,OAAO,GAAG,OAAQ,CAAC,WAAW,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAChE,CAAC,CAAC,mBAAmB;QACrB,CAAC,CAAC,OAAQ,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IAC5B,MAAM,IAAI,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,IAAoB,CAAC,CAAC,sBAAsB;IAE1E,2EAA2E;IAC3E,MAAM,GAAG,GAAG,IAAI,YAAY,CAAC,SAAS,CAAC,CAAC;IACxC,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7B,MAAM,CAAC,GAAG,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;QAC/B,IAAI,CAAC,CAAC;YAAE,SAAS;QACjB,OAAO,IAAI,CAAC,CAAC;QACb,MAAM,IAAI,GAAG,CAAC,GAAG,SAAS,CAAC;QAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE;YAAE,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;IACnE,CAAC;IACD,MAAM,KAAK,GAAG,OAAO,IAAI,CAAC,CAAC;IAC3B,IAAI,IAAI,GAAG,CAAC,CAAC;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;QACnC,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC;QAChB,IAAI,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC;IAC1B,CAAC;IACD,IAAI,GAAG,IAAI,CAAC,IAAI,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package/dist/index.js

@@ -11,7 +11,8 @@ import { z } from "zod";
 import { isReadOnly } from "./config.js";
 import { appendNote, buildIndex, createNote, deleteNote, getOutline, listNotes, listTags, listTodos, moveNote, notesDir, readNote, searchNotes, } from "./store.js";
 import { brokenLinks, findPath, getBacklinks, getNeighbors, graphOverview, relatedNotes, } from "./graph.js";
-const server = new McpServer({ name: "mcp-notes-server", version: "0.2.0" });
+import { semanticSearch } from "./semantic.js";
+const server = new McpServer({ name: "mcp-notes-server", version: "0.3.0" });
 const text = (value) => ({ content: [{ type: "text", text: value }] });
 const fail = (err) => text(`Error: ${err.message}`);
 // --- Read & discovery tools (always registered) --------------------------
@@ -177,6 +178,28 @@ server.registerTool("broken_links", {
         return text("No broken links. 🎉");
     return text(`${broken.length} broken link(s):\n${broken.map((b) => `- ${b.from} → [[${b.target}]]`).join("\n")}`);
 });
+server.registerTool("semantic_search", {
+    title: "Semantic search",
+    description: "Search notes by meaning using local embeddings (all-MiniLM-L6-v2, runs " +
+        "offline after a one-time model download). Finds related notes even with no " +
+        "shared keywords. `hybrid` fuses this with keyword search for best results.",
+    inputSchema: {
+        query: z.string().describe("Natural-language query"),
+        limit: z.number().int().positive().max(100).optional().describe("Max results (default 10)"),
+        hybrid: z.boolean().optional().describe("Fuse semantic + keyword ranking (default false)"),
+    },
+}, async ({ query, limit, hybrid }) => {
+    try {
+        const r = await semanticSearch(query, { limit, hybrid });
+        if (r.hits.length === 0)
+            return text(`No semantic matches for "${query}".`);
+        const lines = r.hits.map((h) => `- ${h.name} (score ${h.score.toFixed(3)})${h.snippet ? `\n    ${h.snippet}` : ""}`);
+        return text(`${r.total} result(s)${r.hasMore ? " (more available)" : ""}:\n${lines.join("\n")}`);
+    }
+    catch (err) {
+        return fail(err);
+    }
+});
 // --- Mutating tools (omitted entirely when NOTES_READONLY=1) --------------
 if (!isReadOnly()) {
     server.registerTool("create_note", {
@@ -255,7 +278,7 @@ async function main() {
     await buildIndex(); // load/sync the index before serving any request
     const transport = new StdioServerTransport();
     await server.connect(transport);
-    console.error(`mcp-notes-server v0.2.0 running${isReadOnly() ? " (read-only)" : ""}. Notes dir: ${notesDir()}`);
+    console.error(`mcp-notes-server v0.3.0 running${isReadOnly() ? " (read-only)" : ""}. Notes dir: ${notesDir()}`);
 }
 main().catch((err) => {
     console.error("Fatal error starting mcp-notes-server:", err);

package/dist/index.js.map

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package/dist/semantic.d.ts

@@ -0,0 +1,14 @@
+import { type SearchHit } from "./store.js";
+/**
+ * Rank notes by semantic similarity to `query`. With `hybrid`, fuse the vector
+ * ranking with MiniSearch's lexical ranking via Reciprocal Rank Fusion (k=60).
+ * First call downloads/loads the model and embeds the whole vault.
+ */
+export declare function semanticSearch(query: string, opts?: {
+    limit?: number;
+    hybrid?: boolean;
+}): Promise<{
+    hits: SearchHit[];
+    total: number;
+    hasMore: boolean;
+}>;

package/dist/semantic.js

@@ -0,0 +1,142 @@
+/**
+ * Semantic vector store: keeps an L2-normalized embedding per note, persisted to
+ * a sidecar cache and incrementally synced (mtime/size) against the text index.
+ * Mirrors store.ts's cache+sync pattern. The embedding model is only touched
+ * when a semantic search actually runs (first call embeds the whole vault).
+ */
+import { promises as fs } from "node:fs";
+import { EMBED_CACHE_VERSION, EMBED_DIM, EMBED_MODEL_ID, getEmbeddingsPath, cacheDisabled, } from "./config.js";
+import { atomicWrite, readRaw, resolveSafe } from "./fsutil.js";
+import { parseNote } from "./parse.js";
+import { embed } from "./embed.js";
+import { getAllMeta, searchNotes } from "./store.js";
+const vectors = new Map();
+let cacheLoaded = false;
+function encodeVec(v) {
+    return Buffer.from(v.buffer, v.byteOffset, v.byteLength).toString("base64");
+}
+function decodeVec(b64) {
+    const buf = Buffer.from(b64, "base64");
+    return new Float32Array(buf.buffer, buf.byteOffset, buf.byteLength / 4);
+}
+/** Load the persisted vectors once (ignored if model/dim/version changed). */
+async function loadCache() {
+    if (cacheLoaded || cacheDisabled()) {
+        cacheLoaded = true;
+        return;
+    }
+    cacheLoaded = true;
+    try {
+        const cache = JSON.parse(await fs.readFile(getEmbeddingsPath(), "utf8"));
+        if (cache.version !== EMBED_CACHE_VERSION || cache.model !== EMBED_MODEL_ID || cache.dim !== EMBED_DIM) {
+            return; // stale → will be rebuilt by sync
+        }
+        for (const [name, e] of Object.entries(cache.perNote ?? {})) {
+            vectors.set(name, { mtimeMs: e.mtimeMs, size: e.size, vec: decodeVec(e.vector) });
+        }
+    }
+    catch (err) {
+        if (err.code !== "ENOENT") {
+            console.error(`Embeddings cache unreadable, rebuilding: ${err.message}`);
+        }
+    }
+}
+async function writeCache() {
+    if (cacheDisabled())
+        return;
+    const perNote = {};
+    for (const [name, e] of vectors)
+        perNote[name] = { mtimeMs: e.mtimeMs, size: e.size, vector: encodeVec(e.vec) };
+    const cache = { version: EMBED_CACHE_VERSION, model: EMBED_MODEL_ID, dim: EMBED_DIM, perNote };
+    try {
+        await atomicWrite(getEmbeddingsPath(), JSON.stringify(cache));
+    }
+    catch (err) {
+        console.error(`Could not write embeddings cache: ${err.message}`);
+    }
+}
+/** Embed new/changed notes, drop deleted ones, persist if anything changed. */
+async function sync() {
+    await loadCache();
+    const meta = getAllMeta();
+    let changed = false;
+    for (const [name, m] of meta) {
+        const prev = vectors.get(name);
+        if (prev && prev.mtimeMs === m.mtimeMs && prev.size === m.size)
+            continue;
+        try {
+            const { title, body } = parseNote(await readRaw(await resolveSafe(name)));
+            const vec = await embed(`${title ?? name}\n${body}`);
+            vectors.set(name, { mtimeMs: m.mtimeMs, size: m.size, vec });
+            changed = true;
+        }
+        catch (err) {
+            console.error(`Could not embed "${name}": ${err.message}`);
+        }
+    }
+    for (const name of [...vectors.keys()]) {
+        if (!meta.has(name)) {
+            vectors.delete(name);
+            changed = true;
+        }
+    }
+    if (changed)
+        await writeCache();
+}
+function dot(a, b) {
+    let s = 0;
+    for (let i = 0; i < EMBED_DIM; i++)
+        s += a[i] * b[i];
+    return s;
+}
+function snippet(body, width = 160) {
+    const flat = body.replace(/\s+/g, " ").trim();
+    return flat.length > width ? `${flat.slice(0, width)}…` : flat;
+}
+async function snippetFor(name) {
+    try {
+        return snippet(parseNote(await readRaw(await resolveSafe(name))).body);
+    }
+    catch {
+        return "";
+    }
+}
+/**
+ * Rank notes by semantic similarity to `query`. With `hybrid`, fuse the vector
+ * ranking with MiniSearch's lexical ranking via Reciprocal Rank Fusion (k=60).
+ * First call downloads/loads the model and embeds the whole vault.
+ */
+export async function semanticSearch(query, opts = {}) {
+    const limit = opts.limit ?? 10;
+    await sync();
+    const qv = await embed(query);
+    const ranked = [...vectors.entries()]
+        .map(([name, e]) => ({ name, score: dot(qv, e.vec) }))
+        .sort((a, b) => b.score - a.score);
+    let order;
+    if (opts.hybrid) {
+        const K = 60;
+        const fused = new Map();
+        ranked.slice(0, 50).forEach((r, i) => fused.set(r.name, (fused.get(r.name) ?? 0) + 1 / (K + i + 1)));
+        const lexical = await searchNotes(query, { limit: 50 });
+        lexical.hits.forEach((h, i) => fused.set(h.name, (fused.get(h.name) ?? 0) + 1 / (K + i + 1)));
+        order = [...fused.entries()].map(([name, score]) => ({ name, score })).sort((a, b) => b.score - a.score);
+    }
+    else {
+        order = ranked;
+    }
+    const total = order.length;
+    const page = order.slice(0, limit);
+    const meta = getAllMeta();
+    const hits = [];
+    for (const r of page) {
+        hits.push({
+            name: r.name,
+            title: meta.get(r.name)?.title ?? r.name,
+            score: r.score,
+            snippet: await snippetFor(r.name),
+        });
+    }
+    return { hits, total, hasMore: limit < total };
+}
+//# sourceMappingURL=semantic.js.map

package/dist/semantic.js.map

@@ -0,0 +1 @@
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package/dist/tokenizer.d.ts

@@ -0,0 +1,30 @@
+/**
+ * Hand-rolled BERT-uncased WordPiece tokenizer — pure JS, no dependencies.
+ * Mirrors google-research/bert `tokenization.py` (BasicTokenizer +
+ * WordpieceTokenizer) closely enough to feed all-MiniLM-L6-v2. We hand-roll it
+ * for the same reason we hand-roll the frontmatter parser: avoid a native /
+ * audit-heavy dependency (@huggingface/tokenizers is a Rust binding).
+ */
+export declare class WordPieceTokenizer {
+    private vocab;
+    readonly unkId: number;
+    readonly clsId: number;
+    readonly sepId: number;
+    readonly padId: number;
+    constructor(vocabText: string);
+    /** Normalize: strip control chars, pad CJK, lowercase, remove accents (NFD/Mn). */
+    private normalize;
+    /** Whitespace + punctuation split into basic tokens (BERT BasicTokenizer). */
+    private basicTokenize;
+    /** Greedy longest-match-first WordPiece split of a single word. */
+    private wordpiece;
+    /**
+     * Encode text into `[CLS] … [SEP]` token ids (truncated to maxLen) plus an
+     * all-ones attention mask. We embed one text at a time (batch 1), so no
+     * padding is needed.
+     */
+    encode(text: string, maxLen?: number): {
+        inputIds: number[];
+        attentionMask: number[];
+    };
+}

package/dist/tokenizer.js

@@ -0,0 +1,140 @@
+/**
+ * Hand-rolled BERT-uncased WordPiece tokenizer — pure JS, no dependencies.
+ * Mirrors google-research/bert `tokenization.py` (BasicTokenizer +
+ * WordpieceTokenizer) closely enough to feed all-MiniLM-L6-v2. We hand-roll it
+ * for the same reason we hand-roll the frontmatter parser: avoid a native /
+ * audit-heavy dependency (@huggingface/tokenizers is a Rust binding).
+ */
+const SPECIAL = { unk: "[UNK]", cls: "[CLS]", sep: "[SEP]", pad: "[PAD]" };
+/** True if a Unicode code point is a CJK character (BERT `_is_chinese_char`). */
+function isCjk(cp) {
+    return ((cp >= 0x4e00 && cp <= 0x9fff) ||
+        (cp >= 0x3400 && cp <= 0x4dbf) ||
+        (cp >= 0x20000 && cp <= 0x2a6df) ||
+        (cp >= 0x2a700 && cp <= 0x2b73f) ||
+        (cp >= 0x2b740 && cp <= 0x2b81f) ||
+        (cp >= 0x2b820 && cp <= 0x2ceaf) ||
+        (cp >= 0xf900 && cp <= 0xfaff) ||
+        (cp >= 0x2f800 && cp <= 0x2fa1f));
+}
+/** BERT `_is_punctuation`: all non-alphanumeric ASCII + any Unicode P* category. */
+function isPunct(ch) {
+    const cp = ch.codePointAt(0);
+    if ((cp >= 33 && cp <= 47) ||
+        (cp >= 58 && cp <= 64) ||
+        (cp >= 91 && cp <= 96) ||
+        (cp >= 123 && cp <= 126)) {
+        return true;
+    }
+    return /\p{P}/u.test(ch);
+}
+export class WordPieceTokenizer {
+    vocab;
+    unkId;
+    clsId;
+    sepId;
+    padId;
+    constructor(vocabText) {
+        this.vocab = new Map();
+        const lines = vocabText.split(/\r?\n/);
+        let i = 0;
+        for (const line of lines) {
+            // vocab.txt is one token per line; the line number is the id. Do not trim
+            // away a token that is itself whitespace-like — but blank trailing lines
+            // (from the split) must not consume ids, so stop at the first empty tail.
+            const tok = line.replace(/\r$/, "");
+            if (tok === "" && i >= lines.length - 2)
+                break;
+            this.vocab.set(tok, i);
+            i++;
+        }
+        this.unkId = this.vocab.get(SPECIAL.unk);
+        this.clsId = this.vocab.get(SPECIAL.cls);
+        this.sepId = this.vocab.get(SPECIAL.sep);
+        this.padId = this.vocab.get(SPECIAL.pad) ?? 0;
+        if (this.unkId === undefined || this.clsId === undefined || this.sepId === undefined) {
+            throw new Error("vocab.txt is missing required special tokens ([UNK]/[CLS]/[SEP]).");
+        }
+    }
+    /** Normalize: strip control chars, pad CJK, lowercase, remove accents (NFD/Mn). */
+    normalize(text) {
+        let out = "";
+        for (const ch of text) {
+            const cp = ch.codePointAt(0);
+            if (cp === 0 || cp === 0xfffd)
+                continue; // invalid
+            if (cp !== 9 && cp !== 10 && cp !== 13 && cp < 32)
+                continue; // control chars
+            out += isCjk(cp) ? ` ${ch} ` : ch;
+        }
+        return out
+            .toLowerCase()
+            .normalize("NFD")
+            .replace(/\p{Mn}/gu, "");
+    }
+    /** Whitespace + punctuation split into basic tokens (BERT BasicTokenizer). */
+    basicTokenize(text) {
+        const tokens = [];
+        for (const word of this.normalize(text).split(/\s+/)) {
+            if (!word)
+                continue;
+            let cur = "";
+            for (const ch of word) {
+                if (isPunct(ch)) {
+                    if (cur) {
+                        tokens.push(cur);
+                        cur = "";
+                    }
+                    tokens.push(ch);
+                }
+                else {
+                    cur += ch;
+                }
+            }
+            if (cur)
+                tokens.push(cur);
+        }
+        return tokens;
+    }
+    /** Greedy longest-match-first WordPiece split of a single word. */
+    wordpiece(word) {
+        if (word.length > 200)
+            return [SPECIAL.unk]; // BERT max_input_chars_per_word
+        const out = [];
+        let start = 0;
+        while (start < word.length) {
+            let end = word.length;
+            let found = null;
+            while (start < end) {
+                const sub = (start > 0 ? "##" : "") + word.slice(start, end);
+                if (this.vocab.has(sub)) {
+                    found = sub;
+                    break;
+                }
+                end--;
+            }
+            if (found === null)
+                return [SPECIAL.unk]; // any unmatchable piece → whole word UNK
+            out.push(found);
+            start = end;
+        }
+        return out;
+    }
+    /**
+     * Encode text into `[CLS] … [SEP]` token ids (truncated to maxLen) plus an
+     * all-ones attention mask. We embed one text at a time (batch 1), so no
+     * padding is needed.
+     */
+    encode(text, maxLen = 256) {
+        const pieceIds = [];
+        for (const tok of this.basicTokenize(text)) {
+            for (const piece of this.wordpiece(tok)) {
+                pieceIds.push(this.vocab.get(piece) ?? this.unkId);
+            }
+        }
+        const body = pieceIds.slice(0, Math.max(0, maxLen - 2));
+        const inputIds = [this.clsId, ...body, this.sepId];
+        return { inputIds, attentionMask: inputIds.map(() => 1) };
+    }
+}
+//# sourceMappingURL=tokenizer.js.map

package/dist/tokenizer.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abhishekmcp/notes",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "description": "MCP server for local markdown notes — ranked search, tags, todos, and a wiki-link knowledge graph, from any MCP client.",
   "type": "module",
   "bin": {
@@ -44,6 +44,7 @@
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.29.0",
     "minisearch": "^7.1.0",
+    "onnxruntime-web": "^1.27.0",
     "zod": "^3.23.8"
   },
   "devDependencies": {