oh-my-second-brain 0.2.0 → 0.6.1

package/dist/kernel/engine/retrieval/rrf.js

@@ -0,0 +1,77 @@
+/**
+ * Reciprocal Rank Fusion (RRF) — k=60 standard implementation.
+ *
+ * Algorithm (idea-only, no verbatim code):
+ *   nashsu/llm_wiki (GPL-3.0) — RRF weight schedule concept.
+ *   MS GraphRAG technical report — k=60 default calibration.
+ *
+ * Formula: score(d) = Σ_i  1 / (k + rank_i(d))
+ * where rank_i(d) is the 1-based position of document d in list i.
+ * Documents absent from a list contribute 0 for that list.
+ */
+function validateRrfInputs(rankedLists, k, options) {
+    if (!Array.isArray(rankedLists)) {
+        throw new Error("RRF ranked lists must be an array.");
+    }
+    if (options === null || typeof options !== "object" || Array.isArray(options)) {
+        throw new Error("RRF options must be an object.");
+    }
+    if (!Number.isFinite(k) || k < 0) {
+        throw new Error("RRF smoothing constant k must be a finite non-negative number.");
+    }
+    if (typeof options.preserveInputOrder !== "undefined" && typeof options.preserveInputOrder !== "boolean") {
+        throw new Error("RRF preserveInputOrder must be a boolean.");
+    }
+    for (const list of rankedLists) {
+        if (!Array.isArray(list)) {
+            throw new Error("RRF ranked lists must be arrays of scored hits.");
+        }
+        for (const hit of list) {
+            if (hit === null ||
+                typeof hit !== "object" ||
+                typeof hit.docPath !== "string" ||
+                hit.docPath.trim().length === 0 ||
+                !Number.isSafeInteger(hit.chunkOrdinal) ||
+                hit.chunkOrdinal < 0 ||
+                !Number.isFinite(hit.score)) {
+                throw new Error("RRF scored hits must have a non-empty path, non-negative ordinal, and finite score.");
+            }
+        }
+    }
+}
+export function fuseRRF(rankedLists, k = 60, options = {}) {
+    validateRrfInputs(rankedLists, k, options);
+    if (rankedLists.length === 0)
+        return [];
+    // key → { accumulated RRF score, original hit metadata }
+    const accum = new Map();
+    for (const list of rankedLists) {
+        if (list.length === 0)
+            continue;
+        // Dispatch policies may establish rank independently of raw score. In that
+        // case, preserve the caller's order rather than replacing it here.
+        const sorted = options.preserveInputOrder
+            ? list
+            : [...list].sort((a, b) => b.score - a.score ||
+                a.docPath.localeCompare(b.docPath) ||
+                a.chunkOrdinal - b.chunkOrdinal);
+        for (let idx = 0; idx < sorted.length; idx++) {
+            const hit = sorted[idx];
+            const key = `${hit.docPath}\x00${hit.chunkOrdinal}`;
+            // idx is 0-based; rank is 1-based → 1/(k + idx + 1)
+            const contribution = 1 / (k + idx + 1);
+            const existing = accum.get(key);
+            if (existing !== undefined) {
+                existing.score += contribution;
+            }
+            else {
+                accum.set(key, { score: contribution, hit });
+            }
+        }
+    }
+    return [...accum.values()]
+        .sort((a, b) => b.score - a.score ||
+        `${a.hit.docPath}\x00${a.hit.chunkOrdinal}`.localeCompare(`${b.hit.docPath}\x00${b.hit.chunkOrdinal}`))
+        .map(({ score, hit }) => ({ ...hit, score }));
+}
+//# sourceMappingURL=rrf.js.map

package/dist/kernel/engine/retrieval/rrf.js.map

@@ -0,0 +1 @@
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package/dist/{engine → kernel/engine}/tracer.d.ts

@@ -13,11 +13,24 @@
  *     → typed queries (C3) → RRF → RetrievalResult[]
  */
 import type { EngineConfig, RetrievalResult, TypedSubQuery } from "./types.js";
+import type { EmbeddingModelDescriptor } from "./embed/model.js";
 /**
  * Configuration for a single runTracer() invocation.
  * Extends the shared EngineConfig with tracer-specific options.
  */
 export interface TracerConfig extends EngineConfig {
+    /**
+     * Canonical setup descriptor.  The descriptor is carried alongside the
+     * scalar config so model width/context and preprocessing metadata are not
+     * discarded when the tracer composes the provider.
+     */
+    embeddingDescriptor?: EmbeddingModelDescriptor | null;
+    embeddingContext?: number;
+    embeddingContextLength?: number;
+    embeddingContextTokens?: number;
+    embeddingMrlDim?: number;
+    embeddingNormalization?: string;
+    embeddingPrefixScheme?: string;
     /**
      * Vault-relative file paths to process in this run.
      * When absent, the entire vault is walked recursively.

package/dist/{engine → kernel/engine}/tracer.js

@@ -76,12 +76,29 @@ export async function runTracer(config, queries) {
     // ── Step 1: resolve vault files ───────────────────────────────────────────
     const files = await resolveFiles(vaultPath, config.files);
     // ── Step 2: create embed provider + store ─────────────────────────────────
+    const descriptor = config.embeddingDescriptor ?? undefined;
+    const embeddingProvider = config.embeddingProvider ?? descriptor?.provider;
+    const embeddingModel = config.embeddingModel ??
+        descriptor?.path ??
+        descriptor?.modelPath ??
+        descriptor?.model;
     const embedProvider = requireRealEmbeddingProvider({
-        provider: config.embeddingProvider,
-        model: config.embeddingModel,
+        provider: embeddingProvider,
+        model: embeddingModel,
+        dimensions: config.embeddingDimensions ?? descriptor?.dimensions,
+        context: config.embeddingContext ?? descriptor?.context,
+        contextLength: config.embeddingContextLength ?? descriptor?.contextLength,
+        contextTokens: config.embeddingContextTokens ?? descriptor?.contextTokens,
+        mrlDim: config.embeddingMrlDim ?? descriptor?.mrlDim,
+        normalization: config.embeddingNormalization ?? descriptor?.normalization,
+        prefixScheme: config.embeddingPrefixScheme ?? descriptor?.prefixScheme,
     });
     await mkdir(path.dirname(config.dbPath), { recursive: true });
-    const store = openEngineStore(config.dbPath, config.embeddingDimensions);
+    // A descriptor is authoritative for its vector width when no scalar
+    // override was supplied.  Falling back to the provider width keeps custom
+    // providers usable without inventing a dimension in the tracer.
+    const dimensions = config.embeddingDimensions ?? descriptor?.dimensions ?? embedProvider.dimensions;
+    const store = openEngineStore(config.dbPath, dimensions);
     try {
         // Chunk + embed + upsert every resolved file
         for (const filePath of files) {
@@ -159,12 +176,52 @@ export function resolveVault() {
  */
 export function makeTracerConfig(overrides = {}) {
     const vaultPath = overrides.vaultPath ?? resolveVault();
+    const descriptor = overrides.embeddingDescriptor ?? undefined;
     return {
         vaultPath,
         dbPath: overrides.dbPath ?? path.join(vaultPath, ".oms", "cache", "engine", "engine.db"),
-        embeddingDimensions: overrides.embeddingDimensions ?? 768,
-        embeddingProvider: overrides.embeddingProvider ?? process.env["OMS_EMBEDDING_PROVIDER"],
-        embeddingModel: overrides.embeddingModel ?? process.env["OMS_EMBEDDING_MODEL"],
+        embeddingDimensions: overrides.embeddingDimensions ?? descriptor?.dimensions ?? 768,
+        embeddingProvider: overrides.embeddingProvider ??
+            descriptor?.provider ??
+            process.env["OMS_EMBEDDING_PROVIDER"],
+        embeddingModel: overrides.embeddingModel ??
+            descriptor?.path ??
+            descriptor?.modelPath ??
+            descriptor?.model ??
+            process.env["OMS_EMBEDDING_MODEL"],
+        ...(overrides.embeddingDescriptor !== undefined
+            ? { embeddingDescriptor: overrides.embeddingDescriptor }
+            : {}),
+        ...(overrides.embeddingContext !== undefined
+            ? { embeddingContext: overrides.embeddingContext }
+            : descriptor?.context !== undefined
+                ? { embeddingContext: descriptor.context }
+                : {}),
+        ...(overrides.embeddingContextLength !== undefined
+            ? { embeddingContextLength: overrides.embeddingContextLength }
+            : descriptor?.contextLength !== undefined
+                ? { embeddingContextLength: descriptor.contextLength }
+                : {}),
+        ...(overrides.embeddingContextTokens !== undefined
+            ? { embeddingContextTokens: overrides.embeddingContextTokens }
+            : descriptor?.contextTokens !== undefined
+                ? { embeddingContextTokens: descriptor.contextTokens }
+                : {}),
+        ...(overrides.embeddingMrlDim !== undefined
+            ? { embeddingMrlDim: overrides.embeddingMrlDim }
+            : descriptor?.mrlDim !== undefined
+                ? { embeddingMrlDim: descriptor.mrlDim }
+                : {}),
+        ...(overrides.embeddingNormalization !== undefined
+            ? { embeddingNormalization: overrides.embeddingNormalization }
+            : descriptor?.normalization !== undefined
+                ? { embeddingNormalization: descriptor.normalization }
+                : {}),
+        ...(overrides.embeddingPrefixScheme !== undefined
+            ? { embeddingPrefixScheme: overrides.embeddingPrefixScheme }
+            : descriptor?.prefixScheme !== undefined
+                ? { embeddingPrefixScheme: descriptor.prefixScheme }
+                : {}),
         files: overrides.files,
         cacheDir: overrides.cacheDir,
         topK: overrides.topK ?? 10,

package/dist/kernel/engine/tracer.js.map

@@ -0,0 +1 @@
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package/dist/{engine → kernel/engine}/types.d.ts

@@ -82,10 +82,10 @@ export interface VectorStore {
     upsert(rows: ReadonlyArray<Chunk & {
         vector: Float32Array;
     }>): void;
-    /** ANN search: return the `k` nearest chunks to `vec`. */
-    queryVec(vec: Float32Array, k: number): ScoredHit[];
-    /** BM25 lexical search: return the top `k` chunks matching `text`. */
-    queryLex(text: string, k: number): ScoredHit[];
+    /** ANN search: return the `k` nearest chunks to `vec`, optionally scoped by path prefix. */
+    queryVec(vec: Float32Array, k: number, collection?: string): ScoredHit[];
+    /** BM25 lexical search: return the top `k` chunks matching `text`, optionally scoped by path prefix. */
+    queryLex(text: string, k: number, collection?: string): ScoredHit[];
     /** Flush WAL and release the database connection. */
     close(): void;
 }

package/dist/kernel/engine/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/kernel/engine/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG"}

package/dist/{graph → kernel/graph}/cache.d.ts

@@ -1,4 +1,4 @@
-import type { Ontology } from "../core/ontology/types.js";
+import type { Ontology } from "../ontology/types.js";
 export type GraphEdgeType = "folder-concept" | "property-axis" | "property-value" | "wikilink";
 export interface GraphEdge {
     type: GraphEdgeType;

package/dist/{graph → kernel/graph}/cache.js

@@ -1,34 +1,108 @@
 import { createHash } from "node:crypto";
-import { mkdir, readFile, readdir, stat, writeFile } from "node:fs/promises";
+import { mkdir, lstat, readFile, readdir, realpath, rename, stat, unlink, writeFile, } from "node:fs/promises";
 import path from "node:path";
 import { parseNote } from "../conventions/frontmatter.js";
 import { validateFrontmatter } from "../conventions/validate.js";
 import { safeVaultNotePath } from "../capture/safe.js";
-import { resolveConcept } from "../core/ontology/resolver.js";
+import { resolveConcept } from "../ontology/resolver.js";
 const CACHE_VERSION = 1;
 export function graphCachePath(vault) {
-    return path.join(vault, ".oms", "cache", "graph.json");
+    return path.resolve(vault, ".oms", "cache", "graph.json");
 }
 function hash(value) {
     return createHash("sha256").update(value).digest("hex");
 }
-async function* walkMarkdown(dir, base) {
+function ensureInsideRoot(root, candidate, label) {
+    const relative = path.relative(root, candidate);
+    if (relative === ".." || relative.startsWith(`..${path.sep}`) || path.isAbsolute(relative)) {
+        throw new Error(`${label} escapes the configured vault root.`);
+    }
+}
+function isRecord(value) {
+    return value !== null && typeof value === "object" && !Array.isArray(value);
+}
+function isGraphCacheShape(value) {
+    if (!isRecord(value))
+        return false;
+    if (value.version !== CACHE_VERSION ||
+        typeof value.generatedAt !== "string" ||
+        !Array.isArray(value.sourceOfTruth) ||
+        !value.sourceOfTruth.every((item) => typeof item === "string") ||
+        !Array.isArray(value.notes) ||
+        !Array.isArray(value.edges) ||
+        !Array.isArray(value.search) ||
+        !isRecord(value.signatures)) {
+        return false;
+    }
+    const signatures = value.signatures;
+    if (typeof signatures.taxonomyHash !== "string" ||
+        !isRecord(signatures.conceptHashes) ||
+        !isRecord(signatures.notes)) {
+        return false;
+    }
+    for (const note of value.notes) {
+        if (!isRecord(note) ||
+            typeof note.path !== "string" ||
+            typeof note.folder !== "string" ||
+            !(typeof note.concept === "string" || note.concept === null) ||
+            !isRecord(note.frontmatter) ||
+            !isRecord(note.axes) ||
+            !Array.isArray(note.wikilinks) ||
+            !note.wikilinks.every((item) => typeof item === "string") ||
+            note.bodyLoaded !== false ||
+            !isRecord(note.validation) ||
+            typeof note.validation.valid !== "boolean" ||
+            typeof note.validation.violations !== "number") {
+            return false;
+        }
+    }
+    for (const edge of value.edges) {
+        if (!isRecord(edge) ||
+            typeof edge.type !== "string" ||
+            typeof edge.from !== "string" ||
+            typeof edge.to !== "string") {
+            return false;
+        }
+    }
+    for (const document of value.search) {
+        if (!isRecord(document) ||
+            typeof document.path !== "string" ||
+            !Array.isArray(document.terms) ||
+            !document.terms.every((item) => typeof item === "string") ||
+            typeof document.bodyPreview !== "string") {
+            return false;
+        }
+    }
+    return true;
+}
+async function* walkMarkdown(dir, base, rootRealPath, visitedDirectories = new Set()) {
+    const root = rootRealPath ?? await realpath(base);
+    const realDir = await realpath(dir);
+    ensureInsideRoot(root, realDir, `Vault directory "${dir}"`);
+    if (visitedDirectories.has(realDir))
+        return;
+    visitedDirectories.add(realDir);
     let entries;
     try {
         entries = await readdir(dir, { withFileTypes: true });
     }
-    catch {
-        return;
+    catch (error) {
+        throw new Error(`Unable to scan vault directory "${dir}": ${error instanceof Error ? error.message : String(error)}`, { cause: error });
     }
     for (const entry of entries) {
+        const full = path.join(dir, entry.name);
+        // Resolve every entry, including skipped dot-directories, so an escape
+        // cannot hide behind the scanner's exclusion policy.
+        const realEntry = await realpath(full);
+        ensureInsideRoot(root, realEntry, `Vault entry "${full}"`);
         if (entry.name === ".oms" || entry.name === "node_modules" || entry.name.startsWith(".")) {
             continue;
         }
-        const full = path.join(dir, entry.name);
-        if (entry.isDirectory()) {
-            yield* walkMarkdown(full, base);
+        const entryStat = await stat(full);
+        if (entryStat.isDirectory()) {
+            yield* walkMarkdown(full, base, root, visitedDirectories);
         }
-        else if (entry.isFile() && entry.name.endsWith(".md")) {
+        else if (entryStat.isFile() && entry.name.toLowerCase().endsWith(".md")) {
             yield path.relative(base, full).replace(/\\/g, "/");
         }
     }
@@ -87,12 +161,19 @@ function conceptSchemaHash(concept) {
 function taxonomyHash(ontology) {
     return hash(jsonStable(ontology.taxonomy));
 }
+function parseGraphFrontmatter(raw, notePath) {
+    const parsed = parseNote(raw);
+    if (parsed.diagnostics.length > 0) {
+        throw new Error(`${notePath}: malformed frontmatter (${parsed.diagnostics.map((item) => item.message).join("; ")})`);
+    }
+    return parsed;
+}
 async function buildSourceSignatures(vault, ontology) {
     const notes = {};
     for await (const notePath of walkMarkdown(vault, vault)) {
         const fullPath = path.join(vault, notePath);
         const [raw, fileStat] = await Promise.all([readFile(fullPath, "utf-8"), stat(fullPath)]);
-        const parsed = parseNote(raw);
+        const parsed = parseGraphFrontmatter(raw, notePath);
         const wikilinks = extractWikilinks(parsed.body);
         notes[notePath] = {
             mtimeMs: fileStat.mtimeMs,
@@ -112,7 +193,7 @@ async function buildSourceSignatures(vault, ontology) {
     };
 }
 function buildNoteGraph(notePath, raw, ontology) {
-    const parsed = parseNote(raw);
+    const parsed = parseGraphFrontmatter(raw, notePath);
     const folder = firstFolder(notePath);
     const concept = resolveConcept(ontology, notePath);
     const axes = {};
@@ -193,20 +274,76 @@ export async function buildGraphCache(opts) {
     };
     if (opts.write) {
         const outPath = graphCachePath(vault);
-        await mkdir(path.dirname(outPath), { recursive: true });
-        await writeFile(outPath, `${JSON.stringify(cache, null, 2)}\n`, "utf-8");
+        const cacheDirectory = path.dirname(outPath);
+        await mkdir(cacheDirectory, { recursive: true });
+        const rootRealPath = await realpath(vault);
+        const cacheDirectoryRealPath = await realpath(cacheDirectory);
+        ensureInsideRoot(rootRealPath, cacheDirectoryRealPath, "Graph cache directory");
+        const temporaryPath = path.join(cacheDirectory, `.${path.basename(outPath)}.${process.pid}-${Date.now()}-${Math.random().toString(16).slice(2)}.tmp`);
+        try {
+            await writeFile(temporaryPath, `${JSON.stringify(cache, null, 2)}\n`, {
+                encoding: "utf-8",
+                flag: "wx",
+            });
+            await rename(temporaryPath, outPath);
+        }
+        finally {
+            try {
+                await unlink(temporaryPath);
+            }
+            catch (error) {
+                if (error.code !== "ENOENT")
+                    throw error;
+            }
+        }
     }
     return cache;
 }
 export async function readGraphCache(vault) {
+    const root = path.resolve(vault);
+    const rootRealPath = await realpath(root);
+    const cachePath = graphCachePath(root);
+    let cacheDirectoryRealPath;
     try {
-        const raw = await readFile(graphCachePath(vault), "utf-8");
-        const parsed = JSON.parse(raw);
-        return parsed.version === CACHE_VERSION ? parsed : null;
+        cacheDirectoryRealPath = await realpath(path.dirname(cachePath));
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return null;
+        throw error;
+    }
+    ensureInsideRoot(rootRealPath, cacheDirectoryRealPath, "Graph cache directory");
+    let cacheRealPath;
+    try {
+        cacheRealPath = await realpath(cachePath);
+    }
+    catch (error) {
+        if (error.code === "ENOENT") {
+            try {
+                await lstat(cachePath);
+            }
+            catch (missingError) {
+                if (missingError.code === "ENOENT")
+                    return null;
+                throw missingError;
+            }
+            throw new Error(`Graph cache "${cachePath}" is a broken symbolic link.`, { cause: error });
+        }
+        throw error;
+    }
+    ensureInsideRoot(rootRealPath, cacheRealPath, "Graph cache");
+    const raw = await readFile(cachePath, "utf-8");
+    let parsed;
+    try {
+        parsed = JSON.parse(raw);
+    }
+    catch (error) {
+        throw new Error(`Graph cache "${cachePath}" is not valid JSON.`, { cause: error });
     }
-    catch {
-        return null;
+    if (!isGraphCacheShape(parsed)) {
+        throw new Error(`Graph cache "${cachePath}" has an invalid format.`);
     }
+    return parsed;
 }
 function compareSignatures(previous, current) {
     const reasons = [];
@@ -268,6 +405,9 @@ export async function graphCacheStatus(vault, ontology) {
     const cache = await readGraphCache(vault);
     const cachePath = graphCachePath(vault);
     if (!cache) {
+        // Even without a persisted cache, validate source notes so malformed YAML
+        // cannot be silently reported as an ordinary cache miss.
+        await buildSourceSignatures(vault, ontology);
         return {
             cachePath,
             exists: false,
@@ -296,8 +436,12 @@ export async function graphCacheStatus(vault, ontology) {
     };
 }
 export async function lazyLoadNoteBody(vault, notePath) {
-    const resolved = safeVaultNotePath(vault, notePath);
-    const relative = path.relative(vault, resolved);
+    const root = path.resolve(vault);
+    const rootRealPath = await realpath(root);
+    const resolved = safeVaultNotePath(root, notePath);
+    const realResolved = await realpath(resolved);
+    ensureInsideRoot(rootRealPath, realResolved, `Vault note "${notePath}"`);
+    const relative = path.relative(root, resolved);
     const raw = await readFile(resolved, "utf-8");
     return { path: relative.replace(/\\/g, "/"), body: parseNote(raw).body };
 }

package/dist/kernel/graph/cache.js.map

@@ -0,0 +1 @@
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package/dist/kernel/graph/explore.js.map

@@ -0,0 +1 @@
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package/dist/{harness → kernel/harness}/surface-registry.d.ts

@@ -47,7 +47,6 @@ export interface HarnessPackageAssetSurface {
 }
 export interface HarnessSurfaceRegistry {
     readonly cliCommands: readonly HarnessCliCommandSurface[];
-    readonly coreSkillDirs: readonly string[];
     readonly mcpTools: readonly HarnessMcpToolSurface[];
     readonly hosts: readonly HarnessHostSurface[];
     readonly hooks: readonly HarnessHookSurface[];