daftari 1.0.0

package/dist/search/vector.js

@@ -0,0 +1,128 @@
+// Vector (semantic) search half of hybrid search.
+//
+// Documents are split into chunks; each chunk is embedded into a 384-dim
+// vector with the all-MiniLM-L6-v2 sentence-transformer (run locally via
+// @huggingface/transformers — no network at query time once the model is cached).
+// Similarity is cosine distance. Embeddings come back L2-normalised, so cosine
+// reduces to a dot product, but cosineSimilarity stays general for safety.
+//
+// The model loads lazily and is memoised for the process. Loading can fail
+// (e.g. no network on first run, before the model is cached); embed() surfaces
+// that as Result.err so the caller can fall back to lexical-only ranking.
+import { err, ok } from "../frontmatter/types.js";
+export const EMBEDDING_MODEL = "Xenova/all-MiniLM-L6-v2";
+export const EMBEDDING_DIM = 384;
+const CHUNK_MAX_CHARS = 800;
+// Splits a document body into embeddable chunks. Paragraphs (blank-line
+// separated) are packed greedily up to CHUNK_MAX_CHARS; a single paragraph
+// longer than the cap is hard-split. Always returns at least one chunk so an
+// empty body still produces a (possibly empty) vector slot.
+export function chunkText(text) {
+    const paragraphs = text
+        .split(/\n\s*\n/)
+        .map((p) => p.trim())
+        .filter((p) => p.length > 0);
+    const chunks = [];
+    let current = "";
+    for (const para of paragraphs) {
+        if (para.length > CHUNK_MAX_CHARS) {
+            if (current) {
+                chunks.push(current);
+                current = "";
+            }
+            for (let i = 0; i < para.length; i += CHUNK_MAX_CHARS) {
+                chunks.push(para.slice(i, i + CHUNK_MAX_CHARS));
+            }
+            continue;
+        }
+        if (current.length + para.length + 2 > CHUNK_MAX_CHARS && current) {
+            chunks.push(current);
+            current = para;
+        }
+        else {
+            current = current ? `${current}\n\n${para}` : para;
+        }
+    }
+    if (current)
+        chunks.push(current);
+    return chunks.length > 0 ? chunks : [text.trim()];
+}
+// Cosine similarity in [-1, 1]. Mismatched lengths or a zero vector yield 0.
+export function cosineSimilarity(a, b) {
+    if (a.length !== b.length || a.length === 0)
+        return 0;
+    let dot = 0;
+    let normA = 0;
+    let normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        const x = a[i];
+        const y = b[i];
+        dot += x * y;
+        normA += x * x;
+        normB += y * y;
+    }
+    if (normA === 0 || normB === 0)
+        return 0;
+    return dot / (Math.sqrt(normA) * Math.sqrt(normB));
+}
+// Mean of a set of vectors — used to represent a whole document by averaging
+// its chunk embeddings. Returns null when there is nothing to average.
+export function meanEmbedding(vectors) {
+    if (vectors.length === 0)
+        return null;
+    const dim = vectors[0]?.length ?? 0;
+    if (dim === 0)
+        return null;
+    const sum = new Float32Array(dim);
+    for (const v of vectors) {
+        if (v.length !== dim)
+            continue;
+        for (let i = 0; i < dim; i++)
+            sum[i] = sum[i] + v[i];
+    }
+    for (let i = 0; i < dim; i++)
+        sum[i] = sum[i] / vectors.length;
+    return sum;
+}
+let extractorPromise = null;
+async function getExtractor() {
+    if (!extractorPromise) {
+        extractorPromise = import("@huggingface/transformers").then(({ pipeline }) => pipeline("feature-extraction", EMBEDDING_MODEL));
+    }
+    return extractorPromise;
+}
+// Embeds a batch of texts. The whole batch goes through the model in one call.
+// Returns one Float32Array per input text. An empty input yields an empty
+// array without loading the model.
+export async function embed(texts) {
+    if (texts.length === 0)
+        return ok([]);
+    try {
+        const extractor = await getExtractor();
+        const output = await extractor(texts, {
+            pooling: "mean",
+            normalize: true,
+        });
+        const dim = output.dims[output.dims.length - 1] ?? EMBEDDING_DIM;
+        const vectors = [];
+        for (let i = 0; i < texts.length; i++) {
+            vectors.push(output.data.slice(i * dim, (i + 1) * dim));
+        }
+        return ok(vectors);
+    }
+    catch (e) {
+        const reason = e instanceof Error ? e.message : String(e);
+        return err(new Error(`embedding failed: ${reason}`));
+    }
+}
+// Convenience wrapper for embedding a single query string.
+export async function embedQuery(text) {
+    const result = await embed([text]);
+    if (!result.ok)
+        return result;
+    const first = result.value[0];
+    if (!first)
+        return err(new Error("embedding produced no vector"));
+    return ok(first);
+}
+//# sourceMappingURL=vector.js.map

package/dist/search/vector.js.map

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

@@ -0,0 +1,6 @@
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import { type AccessContext } from "./access/rbac.js";
+export declare const SERVER_NAME = "daftari";
+export declare const SERVER_VERSION: string;
+export declare function createServer(vaultRoot: string, access?: AccessContext): Server;
+//# sourceMappingURL=server.d.ts.map

package/dist/server.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,MAAM,EAAE,MAAM,2CAA2C,CAAC;AAEnE,OAAO,EAAE,KAAK,aAAa,EAAe,MAAM,kBAAkB,CAAC;AAMnE,eAAO,MAAM,WAAW,YAAY,CAAC;AAQrC,eAAO,MAAM,cAAc,QAAmB,CAAC;AAK/C,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,GAAE,aAA6B,GAAG,MAAM,CAqD7F"}

package/dist/server.js

@@ -0,0 +1,72 @@
+// MCP server wiring. Builds a Server, registers the read-path tools, and
+// bridges each tool's Result<T, Error> into the MCP tool-call response shape.
+//
+// Tool handlers never throw; they return Result. The CallTool request handler
+// additionally guards against unexpected throws at the transport boundary so a
+// bug cannot take the stdio connection down.
+import { readFileSync } from "node:fs";
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import { CallToolRequestSchema, ListToolsRequestSchema } from "@modelcontextprotocol/sdk/types.js";
+import { guestAccess } from "./access/rbac.js";
+import { curationTools } from "./tools/curation.js";
+import { readTools } from "./tools/read.js";
+import { searchTools } from "./tools/search.js";
+import { writeTools } from "./tools/write.js";
+export const SERVER_NAME = "daftari";
+// The version is read from the package manifest so it never drifts from the
+// published version. src/server.ts and dist/server.js both sit one level under
+// the package root, so this relative path resolves the same in dev and build.
+const manifest = JSON.parse(readFileSync(new URL("../package.json", import.meta.url), "utf-8"));
+export const SERVER_VERSION = manifest.version;
+// The server runs as one access identity for its whole lifetime — the
+// --user / --role it was started with. Every tool call is enforced against it.
+// Absent an explicit context the server falls back to the deny-all guest.
+export function createServer(vaultRoot, access = guestAccess()) {
+    const server = new Server({ name: SERVER_NAME, version: SERVER_VERSION }, { capabilities: { tools: {} } });
+    const tools = [...readTools, ...searchTools, ...writeTools, ...curationTools];
+    const byName = new Map(tools.map((t) => [t.name, t]));
+    server.setRequestHandler(ListToolsRequestSchema, async () => ({
+        tools: tools.map((t) => ({
+            name: t.name,
+            description: t.description,
+            inputSchema: t.inputSchema,
+        })),
+    }));
+    server.setRequestHandler(CallToolRequestSchema, async (request) => {
+        const name = request.params.name;
+        const tool = byName.get(name);
+        if (!tool) {
+            return {
+                isError: true,
+                content: [{ type: "text", text: `unknown tool: ${name}` }],
+            };
+        }
+        try {
+            const args = (request.params.arguments ?? {});
+            const result = await tool.handler(vaultRoot, args, access);
+            if (!result.ok) {
+                return {
+                    isError: true,
+                    content: [{ type: "text", text: `Error: ${result.error.message}` }],
+                };
+            }
+            return {
+                content: [
+                    {
+                        type: "text",
+                        text: JSON.stringify(result.value, null, 2),
+                    },
+                ],
+            };
+        }
+        catch (e) {
+            const reason = e instanceof Error ? e.message : String(e);
+            return {
+                isError: true,
+                content: [{ type: "text", text: `Unexpected error in ${name}: ${reason}` }],
+            };
+        }
+    });
+    return server;
+}
+//# sourceMappingURL=server.js.map

package/dist/server.js.map

@@ -0,0 +1 @@
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package/dist/storage/index-db.d.ts

@@ -0,0 +1,37 @@
+import Database from "better-sqlite3";
+import { type Result } from "../frontmatter/types.js";
+export type IndexDb = Database.Database;
+export interface IndexedDocument {
+    path: string;
+    title: string;
+    collection: string;
+    domain: string;
+    status: string;
+    confidence: string;
+    updated: string;
+    tags: string[];
+    content: string;
+    tokens: string[];
+}
+export interface IndexedChunk {
+    path: string;
+    chunkIndex: number;
+    text: string;
+    embedding: Float32Array | null;
+}
+export declare function indexDbPath(vaultRoot: string): string;
+export declare function openIndexDb(vaultRoot: string): Result<IndexDb, Error>;
+export declare function clearIndex(db: IndexDb): void;
+export declare function deleteDocument(db: IndexDb, path: string): void;
+export declare function embeddingToBlob(vec: Float32Array): Buffer;
+export declare function blobToEmbedding(blob: Buffer): Float32Array;
+export declare function insertDocument(db: IndexDb, doc: IndexedDocument): void;
+export declare function insertChunk(db: IndexDb, chunk: IndexedChunk): void;
+export declare function setMeta(db: IndexDb, key: string, value: string): void;
+export declare function getAllDocuments(db: IndexDb): IndexedDocument[];
+export declare function getDocument(db: IndexDb, path: string): IndexedDocument | null;
+export declare function getAllChunks(db: IndexDb): IndexedChunk[];
+export declare function getChunksForPath(db: IndexDb, path: string): IndexedChunk[];
+export declare function getMeta(db: IndexDb, key: string): string | null;
+export declare function documentCount(db: IndexDb): number;
+//# sourceMappingURL=index-db.d.ts.map

package/dist/storage/index-db.d.ts.map

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package/dist/storage/index-db.js

@@ -0,0 +1,145 @@
+// SQLite index store for search.
+//
+// The index is a derived cache: it holds nothing the markdown files don't
+// already hold, so .daftari/index.db can be deleted and rebuilt at any time
+// (see search/reindex.ts). Two tables carry the search payload:
+//
+//   documents — one row per markdown file: frontmatter fields, the full body,
+//               and the BM25 token list (JSON).
+//   chunks    — one row per embedded text chunk: the chunk text and its vector
+//               embedding (Float32 BLOB, or NULL when embedding was skipped).
+//
+// A small meta table records index-wide facts (embedding dimension, whether
+// vectors were built, when the index was last rebuilt).
+import { mkdirSync } from "node:fs";
+import { join } from "node:path";
+import Database from "better-sqlite3";
+import { err, ok } from "../frontmatter/types.js";
+// The .daftari control directory is excluded from vault listings, so the index
+// file lives there without ever being mistaken for vault content.
+export function indexDbPath(vaultRoot) {
+    return join(vaultRoot, ".daftari", "index.db");
+}
+const SCHEMA = `
+CREATE TABLE IF NOT EXISTS documents (
+  path        TEXT PRIMARY KEY,
+  title       TEXT NOT NULL,
+  collection  TEXT NOT NULL,
+  domain      TEXT NOT NULL,
+  status      TEXT NOT NULL,
+  confidence  TEXT NOT NULL,
+  updated     TEXT NOT NULL,
+  tags        TEXT NOT NULL,
+  content     TEXT NOT NULL,
+  tokens      TEXT NOT NULL
+);
+CREATE TABLE IF NOT EXISTS chunks (
+  path         TEXT NOT NULL,
+  chunk_index  INTEGER NOT NULL,
+  text         TEXT NOT NULL,
+  embedding    BLOB,
+  PRIMARY KEY (path, chunk_index)
+);
+CREATE TABLE IF NOT EXISTS meta (
+  key   TEXT PRIMARY KEY,
+  value TEXT NOT NULL
+);
+`;
+export function openIndexDb(vaultRoot) {
+    try {
+        mkdirSync(join(vaultRoot, ".daftari"), { recursive: true });
+        const db = new Database(indexDbPath(vaultRoot));
+        db.pragma("journal_mode = WAL");
+        db.exec(SCHEMA);
+        return ok(db);
+    }
+    catch (e) {
+        const reason = e instanceof Error ? e.message : String(e);
+        return err(new Error(`cannot open index db: ${reason}`));
+    }
+}
+// Drops every indexed row. Called at the start of a rebuild so a reindex never
+// leaves rows for files that have since been deleted.
+export function clearIndex(db) {
+    db.exec("DELETE FROM documents; DELETE FROM chunks;");
+}
+// Drops one document and all its chunks. Used by the write path to evict a
+// document's stale rows before re-inserting it: a plain INSERT OR REPLACE on
+// chunks would leave orphaned high-index rows behind if the document shrank.
+export function deleteDocument(db, path) {
+    db.prepare("DELETE FROM documents WHERE path = ?").run(path);
+    db.prepare("DELETE FROM chunks WHERE path = ?").run(path);
+}
+// --- Float32 <-> BLOB ------------------------------------------------------
+export function embeddingToBlob(vec) {
+    return Buffer.from(vec.buffer, vec.byteOffset, vec.byteLength);
+}
+export function blobToEmbedding(blob) {
+    // Copy into a fresh, 4-byte-aligned buffer: a Buffer from SQLite may share a
+    // pool with an arbitrary byteOffset, which Float32Array cannot view directly.
+    const copy = new Uint8Array(blob.length);
+    copy.set(blob);
+    return new Float32Array(copy.buffer);
+}
+// --- writes ----------------------------------------------------------------
+export function insertDocument(db, doc) {
+    db.prepare(`INSERT OR REPLACE INTO documents
+       (path, title, collection, domain, status, confidence, updated, tags, content, tokens)
+     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`).run(doc.path, doc.title, doc.collection, doc.domain, doc.status, doc.confidence, doc.updated, JSON.stringify(doc.tags), doc.content, JSON.stringify(doc.tokens));
+}
+export function insertChunk(db, chunk) {
+    db.prepare(`INSERT OR REPLACE INTO chunks (path, chunk_index, text, embedding)
+     VALUES (?, ?, ?, ?)`).run(chunk.path, chunk.chunkIndex, chunk.text, chunk.embedding ? embeddingToBlob(chunk.embedding) : null);
+}
+export function setMeta(db, key, value) {
+    db.prepare("INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)").run(key, value);
+}
+function rowToDocument(row) {
+    return {
+        path: row.path,
+        title: row.title,
+        collection: row.collection,
+        domain: row.domain,
+        status: row.status,
+        confidence: row.confidence,
+        updated: row.updated,
+        tags: JSON.parse(row.tags),
+        content: row.content,
+        tokens: JSON.parse(row.tokens),
+    };
+}
+export function getAllDocuments(db) {
+    const rows = db.prepare("SELECT * FROM documents ORDER BY path").all();
+    return rows.map(rowToDocument);
+}
+export function getDocument(db, path) {
+    const row = db.prepare("SELECT * FROM documents WHERE path = ?").get(path);
+    return row ? rowToDocument(row) : null;
+}
+function rowToChunk(row) {
+    return {
+        path: row.path,
+        chunkIndex: row.chunk_index,
+        text: row.text,
+        embedding: row.embedding ? blobToEmbedding(row.embedding) : null,
+    };
+}
+export function getAllChunks(db) {
+    const rows = db.prepare("SELECT * FROM chunks ORDER BY path, chunk_index").all();
+    return rows.map(rowToChunk);
+}
+export function getChunksForPath(db, path) {
+    const rows = db
+        .prepare("SELECT * FROM chunks WHERE path = ? ORDER BY chunk_index")
+        .all(path);
+    return rows.map(rowToChunk);
+}
+export function getMeta(db, key) {
+    const row = db.prepare("SELECT value FROM meta WHERE key = ?").get(key);
+    return row ? row.value : null;
+}
+export function documentCount(db) {
+    const row = db.prepare("SELECT COUNT(*) AS n FROM documents").get();
+    return row.n;
+}
+//# sourceMappingURL=index-db.js.map

package/dist/storage/index-db.js.map

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

@@ -0,0 +1,6 @@
+import { type Result } from "../frontmatter/types.js";
+export declare function resolveVaultPath(vaultRoot: string, relativePath: string): Result<string, Error>;
+export declare function directoryExists(path: string): Promise<boolean>;
+export declare function readFile(absolutePath: string): Promise<Result<string, Error>>;
+export declare function listFiles(vaultRoot: string, pattern?: string): Promise<Result<string[], Error>>;
+//# sourceMappingURL=local.d.ts.map

package/dist/storage/local.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"local.d.ts","sourceRoot":"","sources":["../../src/storage/local.ts"],"names":[],"mappings":"AASA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAI/D,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAQ/F;AAED,wBAAsB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOpE;AAED,wBAAsB,QAAQ,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAQnF;AAID,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,OAAO,SAAY,GAClB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,KAAK,CAAC,CAAC,CAalC"}

package/dist/storage/local.js

@@ -0,0 +1,57 @@
+// Local filesystem storage backend.
+//
+// Phase 1 is read-only: list markdown files under a vault root and read their
+// contents. A pluggable backend interface (storage/interface.ts) and the
+// SQLite index (storage/index-db.ts) are deferred to later phases.
+import { readFile as fsReadFile, stat } from "node:fs/promises";
+import { isAbsolute, relative, resolve } from "node:path";
+import { glob } from "glob";
+import { err, ok } from "../frontmatter/types.js";
+// Resolves a vault-relative path to an absolute path, refusing anything that
+// escapes the vault root (path traversal) or resolves to the root itself.
+export function resolveVaultPath(vaultRoot, relativePath) {
+    const root = resolve(vaultRoot);
+    const target = resolve(root, relativePath);
+    const rel = relative(root, target);
+    if (rel === "" || rel.startsWith("..") || isAbsolute(rel)) {
+        return err(new Error(`path escapes vault root: ${relativePath}`));
+    }
+    return ok(target);
+}
+export async function directoryExists(path) {
+    try {
+        const s = await stat(path);
+        return s.isDirectory();
+    }
+    catch {
+        return false;
+    }
+}
+export async function readFile(absolutePath) {
+    try {
+        const content = await fsReadFile(absolutePath, "utf-8");
+        return ok(content);
+    }
+    catch (e) {
+        const reason = e instanceof Error ? e.message : String(e);
+        return err(new Error(`cannot read file: ${reason}`));
+    }
+}
+// Lists files under vaultRoot matching a glob pattern. Returns vault-relative
+// POSIX-style paths, sorted. The .daftari control directory is always excluded.
+export async function listFiles(vaultRoot, pattern = "**/*.md") {
+    try {
+        const matches = await glob(pattern, {
+            cwd: resolve(vaultRoot),
+            nodir: true,
+            posix: true,
+            ignore: ["**/.daftari/**", "**/node_modules/**"],
+        });
+        return ok([...matches].sort());
+    }
+    catch (e) {
+        const reason = e instanceof Error ? e.message : String(e);
+        return err(new Error(`cannot list files: ${reason}`));
+    }
+}
+//# sourceMappingURL=local.js.map

package/dist/storage/local.js.map

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package/dist/tools/curation.d.ts

@@ -0,0 +1,22 @@
+import { type AccessContext } from "../access/rbac.js";
+import { type LintCheckName, type LintFinding } from "../curation/lint.js";
+import { type ProvenanceEntry } from "../curation/provenance.js";
+import { type TensionEntry } from "../curation/tension.js";
+import { type Result } from "../frontmatter/types.js";
+import type { ToolDefinition } from "./read.js";
+export declare function vaultTensionLog(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<TensionEntry, Error>>;
+export interface VaultLintResult {
+    generatedAt: string;
+    filter: LintCheckName | null;
+    checks: Partial<Record<LintCheckName, LintFinding[]>>;
+    totalFindings: number;
+}
+export declare function vaultLint(vaultRoot: string, args?: Record<string, unknown>, access?: AccessContext): Promise<Result<VaultLintResult, Error>>;
+export interface VaultProvenanceResult {
+    path: string;
+    count: number;
+    history: ProvenanceEntry[];
+}
+export declare function vaultProvenance(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<VaultProvenanceResult, Error>>;
+export declare const curationTools: ToolDefinition[];
+//# sourceMappingURL=curation.d.ts.map

package/dist/tools/curation.d.ts.map

@@ -0,0 +1 @@
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