ralph-hero-knowledge-index 0.1.21 → 0.1.24

package/dist/reindex.js

@@ -4,11 +4,13 @@ import { homedir } from "node:os";
 import { KnowledgeDB } from "./db.js";
 import { FtsSearch } from "./search.js";
 import { VectorSearch } from "./vector-search.js";
-import { embed, prepareTextForEmbedding } from "./embedder.js";
+import { embedDocument } from "./embedder.js";
 import { parseDocument } from "./parser.js";
 import { findMarkdownFiles } from "./file-scanner.js";
 import { generateIndexes } from "./generate-indexes.js";
-export async function reindex(dirs, dbPath, generate = false) {
+import { loadConfig } from "./config.js";
+import { loadIgnoreForRoot } from "./ignore.js";
+export async function reindex(dirs, dbPath, generate = false, ignorePatterns) {
     console.log(`Indexing ${dirs.join(", ")} -> ${dbPath}`);
     const db = new KnowledgeDB(dbPath);
     const fts = new FtsSearch(db);
@@ -28,13 +30,17 @@ export async function reindex(dirs, dbPath, generate = false) {
     // Phase 1: Discover files on disk
     const filesOnDisk = [];
     for (const dir of dirs) {
-        const found = findMarkdownFiles(dir);
+        const matcher = loadIgnoreForRoot(dir, ignorePatterns);
+        const found = findMarkdownFiles(dir, matcher);
         console.log(`  ${dir}: ${found.length} files`);
         filesOnDisk.push(...found);
     }
     console.log(`Found ${filesOnDisk.length} total markdown files`);
     const filesOnDiskSet = new Set(filesOnDisk.map(f => resolve(f)));
-    // Phase 1: Delete stale entries for files no longer on disk
+    // Phase 1: Delete stale entries for files no longer on disk.
+    // Chunk rows cascade from documents via ON DELETE CASCADE on chunks.document_id,
+    // but the vec0 virtual table does not participate in FK cascades — we must
+    // explicitly delete chunk-level vec rows via GLOB pattern.
     const syncedPaths = db.getAllSyncPaths();
     let deleted = 0;
     for (const syncedPath of syncedPaths) {
@@ -42,6 +48,8 @@ export async function reindex(dirs, dbPath, generate = false) {
             const id = basename(syncedPath, ".md");
             fts.deleteFtsEntry(id);
             db.deleteDocument(id);
+            vec.deleteChunkVecsByDoc(id);
+            // Also delete any legacy doc-level vec row (pre-chunks schema).
             vec.deleteEmbedding(id);
             db.deleteSyncRecord(syncedPath);
             deleted++;
@@ -114,10 +122,25 @@ export async function reindex(dirs, dbPath, generate = false) {
             db.upsertStubDocument(edge.targetId);
             db.addRelationship(edge.sourceId, edge.targetId, "untyped", edge.context);
         }
-        const text = prepareTextForEmbedding(parsed.title, parsed.tags, parsed.content);
+        // Chunk-aware embedding: emit one embedding per chunk, persist to both
+        // the `chunks` table and the `documents_vec` virtual table with chunk ids
+        // of the form `${doc.id}#c${index}`.
+        //
+        // We first clear any stale chunk rows for this doc_id (the document
+        // body may have shrunk across re-indexes) and stale chunk vec rows (which
+        // don't cascade from the `chunks` table because vec0 is a virtual table).
+        db.db.prepare("DELETE FROM chunks WHERE document_id = ?").run(parsed.id);
+        vec.deleteChunkVecsByDoc(parsed.id);
+        // Drop any pre-chunks schema vec row that used the bare doc id.
+        vec.deleteEmbedding(parsed.id);
         try {
-            const embedding = await embed(text);
-            vec.upsertEmbedding(parsed.id, embedding);
+            const chunks = await embedDocument(parsed.title, parsed.tags, parsed.content);
+            const insertChunk = db.db.prepare("INSERT INTO chunks (id, document_id, chunk_index, content, char_start, char_end) VALUES (?, ?, ?, ?, ?, ?)");
+            for (const chunk of chunks) {
+                const chunkId = `${parsed.id}#c${chunk.index}`;
+                insertChunk.run(chunkId, parsed.id, chunk.index, chunk.content, chunk.charStart, chunk.charEnd);
+                vec.upsertEmbedding(chunkId, chunk.embedding);
+            }
         }
         catch (e) {
             console.warn(`Failed to embed ${id}: ${e.message}`);
@@ -158,28 +181,77 @@ export async function reindex(dirs, dbPath, generate = false) {
     }
 }
 const DEFAULT_DB_PATH = join(homedir(), ".ralph-hero", "knowledge.db");
+/**
+ * Resolve the set of roots, database path, and generate flag for a reindex
+ * run. Precedence (highest to lowest):
+ *   1. CLI positional args
+ *   2. `RALPH_KNOWLEDGE_DIRS` environment variable
+ *   3. `config.roots` from `~/.ralph/knowledge.config.json`
+ *   4. `"../../thoughts"` fallback
+ *
+ * `dbPath` precedence is independent: CLI `.db` positional > `RALPH_KNOWLEDGE_DB`
+ * env var > `config.dbPath` > {@link DEFAULT_DB_PATH}.
+ *
+ * The returned `config` is forwarded to the caller so `ignorePatterns` can be
+ * threaded into {@link reindex}.
+ */
 export function resolveDirs() {
     const cliArgs = process.argv.slice(2);
     const noGenerate = cliArgs.includes("--no-generate");
     const positional = cliArgs.filter(a => !a.startsWith("--"));
     const cliDb = positional.find(a => a.endsWith(".db"));
     const cliDirs = positional.filter(a => !a.endsWith(".db"));
+    const config = loadConfig();
+    const resolveDbPath = () => cliDb ??
+        process.env.RALPH_KNOWLEDGE_DB ??
+        config.dbPath ??
+        DEFAULT_DB_PATH;
     if (cliDirs.length > 0) {
-        return { dirs: cliDirs, dbPath: cliDb ?? DEFAULT_DB_PATH, generate: !noGenerate };
+        console.log("Using roots from: CLI");
+        return {
+            dirs: cliDirs,
+            dbPath: resolveDbPath(),
+            generate: !noGenerate,
+            source: "cli",
+            config,
+        };
     }
     const envDirs = process.env.RALPH_KNOWLEDGE_DIRS;
     if (envDirs) {
+        const parsed = envDirs.split(",").map(d => d.trim()).filter(Boolean);
+        if (parsed.length > 0) {
+            console.log("Using roots from: env");
+            return {
+                dirs: parsed,
+                dbPath: resolveDbPath(),
+                generate: !noGenerate,
+                source: "env",
+                config,
+            };
+        }
+    }
+    if (config.roots && config.roots.length > 0) {
+        console.log("Using roots from: config");
         return {
-            dirs: envDirs.split(",").map(d => d.trim()).filter(Boolean),
-            dbPath: cliDb ?? process.env.RALPH_KNOWLEDGE_DB ?? DEFAULT_DB_PATH,
+            dirs: config.roots,
+            dbPath: resolveDbPath(),
             generate: !noGenerate,
+            source: "config",
+            config,
         };
     }
-    return { dirs: ["../../thoughts"], dbPath: cliDb ?? DEFAULT_DB_PATH, generate: !noGenerate };
+    console.log("Using roots from: fallback");
+    return {
+        dirs: ["../../thoughts"],
+        dbPath: resolveDbPath(),
+        generate: !noGenerate,
+        source: "fallback",
+        config,
+    };
 }
 const isMain = process.argv[1]?.endsWith("reindex.js");
 if (isMain) {
-    const { dirs, dbPath, generate } = resolveDirs();
-    reindex(dirs, dbPath, generate).catch(console.error);
+    const { dirs, dbPath, generate, config } = resolveDirs();
+    reindex(dirs, dbPath, generate, config.ignorePatterns).catch(console.error);
 }
 //# sourceMappingURL=reindex.js.map

package/dist/reindex.js.map

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package/dist/search.d.ts

@@ -1,9 +1,11 @@
 import type { KnowledgeDB } from "./db.js";
+export type MemoryTier = "doc" | "raw" | "reflection" | "any";
 export interface SearchOptions {
     type?: string;
     tags?: string[];
     includeSuperseded?: boolean;
     limit?: number;
+    memoryTier?: MemoryTier;
 }
 export interface SearchResult {
     id: string;
@@ -14,6 +16,11 @@ export interface SearchResult {
     date: string | null;
     score: number;
     snippet: string;
+    chunkIndex?: number;
+    charStart?: number;
+    charEnd?: number;
+    contextPrefix?: string;
+    bestChunkId?: string;
 }
 export declare class FtsSearch {
     private readonly db;
@@ -37,5 +44,10 @@ export declare class FtsSearch {
     ensureTable(): void;
     rebuildIndex(): void;
     private escapeFts5Query;
+    /**
+     * Returns true when the `documents.memory_tier` column exists (schema v3+).
+     * On v2 schemas this is false and the memoryTier filter is silently ignored.
+     */
+    private memoryTierColumnExists;
     search(query: string, options?: SearchOptions): SearchResult[];
 }

package/dist/search.js

@@ -66,8 +66,18 @@ export class FtsSearch {
             return '""';
         return tokens.map(t => '"' + t.replace(/"/g, '""') + '"').join(" ");
     }
+    /**
+     * Returns true when the `documents.memory_tier` column exists (schema v3+).
+     * On v2 schemas this is false and the memoryTier filter is silently ignored.
+     */
+    memoryTierColumnExists() {
+        const rows = this.db.db
+            .prepare("PRAGMA table_info(documents)")
+            .all();
+        return rows.some((r) => r.name === "memory_tier");
+    }
     search(query, options = {}) {
-        const { type, tags, includeSuperseded = false, limit = 20 } = options;
+        const { type, tags, includeSuperseded = false, limit = 20, memoryTier } = options;
         const conditions = ["documents_fts MATCH @query"];
         const params = { query: this.escapeFts5Query(query), limit };
         if (!includeSuperseded) {
@@ -77,6 +87,10 @@ export class FtsSearch {
             conditions.push("d.type = @type");
             params.type = type;
         }
+        if (memoryTier && memoryTier !== "any" && this.memoryTierColumnExists()) {
+            conditions.push("d.memory_tier = @memoryTier");
+            params.memoryTier = memoryTier;
+        }
         let joinClause = "";
         if (tags && tags.length > 0) {
             joinClause = "JOIN tags t ON t.doc_id = d.id";

package/dist/search.js.map

@@ -1 +1 @@
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+{"version":3,"file":"search.js","sourceRoot":"","sources":["../src/search.ts"],"names":[],"mappings":"AA8BA,MAAM,OAAO,SAAS;IACH,EAAE,CAAc;IAEjC,YAAY,EAAe;QACzB,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;IACf,CAAC;IAED;;;;OAIG;IACH,cAAc,CAAC,KAAa;QAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAC5B,gEAAgE,CACjE,CAAC,GAAG,CAAC,KAAK,CAAgF,CAAC;QAC5F,IAAI,CAAC,GAAG;YAAE,OAAO;QACjB,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAChB,oGAAoG,CACrG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;IACrD,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,KAAa;QAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAC5B,gEAAgE,CACjE,CAAC,GAAG,CAAC,KAAK,CAAgF,CAAC;QAC5F,IAAI,CAAC,GAAG;YAAE,OAAO;QACjB,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAChB,2EAA2E,CAC5E,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;IACrD,CAAC;IAED;;;;OAIG;IACH,WAAW;QACT,4DAA4D;QAC5D,MAAM,MAAM,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAC/B,4EAA4E,CAC7E,CAAC,GAAG,EAAE,CAAC;QACR,IAAI,MAAM;YAAE,OAAO;QACnB,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;;;;;;;;KAQf,CAAC,CAAC;IACL,CAAC;IAED,YAAY;QACV,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,oCAAoC,CAAC,CAAC;QACtD,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;;;;;;;;KAQf,CAAC,CAAC;QACH,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;;;KAGf,CAAC,CAAC;IACL,CAAC;IAEO,eAAe,CAAC,GAAW;QACjC,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAChD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,IAAI,CAAC;QACrC,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,EAAE,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACtE,CAAC;IAED;;;OAGG;IACK,sBAAsB;QAC5B,MAAM,IAAI,GAAG,IAAI,CAAC,EAAE,CAAC,EAAE;aACpB,OAAO,CAAC,8BAA8B,CAAC;aACvC,GAAG,EAA6B,CAAC;QACpC,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CAAC,CAAC;IACpD,CAAC;IAED,MAAM,CAAC,KAAa,EAAE,UAAyB,EAAE;QAC/C,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,iBAAiB,GAAG,KAAK,EAAE,KAAK,GAAG,EAAE,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;QAElF,MAAM,UAAU,GAAa,CAAC,4BAA4B,CAAC,CAAC;QAC5D,MAAM,MAAM,GAA4B,EAAE,KAAK,EAAE,IAAI,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,CAAC;QAEtF,IAAI,CAAC,iBAAiB,EAAE,CAAC;YACvB,UAAU,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;QAClD,CAAC;QAED,IAAI,IAAI,EAAE,CAAC;YACT,UAAU,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;YAClC,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;QACrB,CAAC;QAED,IAAI,UAAU,IAAI,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,sBAAsB,EAAE,EAAE,CAAC;YACxE,UAAU,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC;YAC/C,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;QACjC,CAAC;QAED,IAAI,UAAU,GAAG,EAAE,CAAC;QACpB,IAAI,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,UAAU,GAAG,gCAAgC,CAAC;YAC9C,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YACvD,UAAU,CAAC,IAAI,CAAC,aAAa,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC5D,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE;gBACtB,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC;YAC1B,CAAC,CAAC,CAAC;QACL,CAAC;QAED,MAAM,WAAW,GAAG,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QAE7C,MAAM,GAAG,GAAG;;;;;;;;;;;;QAYR,UAAU;cACJ,WAAW;;;KAGpB,CAAC;QAEF,OAAO,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAmB,CAAC;IAC/D,CAAC;CACF"}

package/dist/vector-search.d.ts

@@ -12,5 +12,15 @@ export declare class VectorSearch {
     dropIndex(): void;
     upsertEmbedding(id: string, embedding: Float32Array): void;
     deleteEmbedding(id: string): void;
+    /**
+     * Delete all chunk-level vec rows for a document. Chunk ids follow the
+     * pattern `${docId}#c${index}` so we match via a SQLite GLOB.
+     *
+     * This is used by reindex to drop stale chunks when a source markdown file
+     * has been deleted or modified. Complements `ON DELETE CASCADE` on the
+     * `chunks` table (which deletes chunk rows but not their vec counterparts,
+     * because the vec0 virtual table does not participate in FK cascades).
+     */
+    deleteChunkVecsByDoc(docId: string): void;
     search(queryEmbedding: Float32Array, limit?: number): VectorResult[];
 }

package/dist/vector-search.js

@@ -42,6 +42,21 @@ export class VectorSearch {
             .prepare("DELETE FROM documents_vec WHERE id = ?")
             .run(id);
     }
+    /**
+     * Delete all chunk-level vec rows for a document. Chunk ids follow the
+     * pattern `${docId}#c${index}` so we match via a SQLite GLOB.
+     *
+     * This is used by reindex to drop stale chunks when a source markdown file
+     * has been deleted or modified. Complements `ON DELETE CASCADE` on the
+     * `chunks` table (which deletes chunk rows but not their vec counterparts,
+     * because the vec0 virtual table does not participate in FK cascades).
+     */
+    deleteChunkVecsByDoc(docId) {
+        this.ensureVecLoaded();
+        this.knowledgeDb.db
+            .prepare("DELETE FROM documents_vec WHERE id GLOB ?")
+            .run(`${docId}#c*`);
+    }
     search(queryEmbedding, limit = 10) {
         this.ensureVecLoaded();
         const buf = float32ToBuffer(queryEmbedding);

package/dist/vector-search.js.map

@@ -1 +1 @@
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+{"version":3,"file":"vector-search.js","sourceRoot":"","sources":["../src/vector-search.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,SAAS,MAAM,YAAY,CAAC;AAQxC,SAAS,eAAe,CAAC,GAAiB;IACxC,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,UAAU,EAAE,GAAG,CAAC,UAAU,CAAC,CAAC;AACjE,CAAC;AAED,MAAM,OAAO,YAAY;IAGH;IAFZ,SAAS,GAAG,KAAK,CAAC;IAE1B,YAAoB,WAAwB;QAAxB,gBAAW,GAAX,WAAW,CAAa;IAAG,CAAC;IAExC,eAAe;QACrB,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC;YACpB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC;YACpC,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC;QACxB,CAAC;IACH,CAAC;IAED,WAAW;QACT,IAAI,CAAC,eAAe,EAAE,CAAC;QACvB,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,IAAI,CAAC;;;;;KAKxB,CAAC,CAAC;IACL,CAAC;IAED,SAAS;QACP,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,IAAI,CAAC,oCAAoC,CAAC,CAAC;IACjE,CAAC;IAED,eAAe,CAAC,EAAU,EAAE,SAAuB;QACjD,IAAI,CAAC,eAAe,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,eAAe,CAAC,SAAS,CAAC,CAAC;QACvC,IAAI,CAAC,WAAW,CAAC,EAAE;aAChB,OAAO,CAAC,wCAAwC,CAAC;aACjD,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,IAAI,CAAC,WAAW,CAAC,EAAE;aAChB,OAAO,CAAC,yDAAyD,CAAC;aAClE,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC;IAClB,CAAC;IAED,eAAe,CAAC,EAAU;QACxB,IAAI,CAAC,eAAe,EAAE,CAAC;QACvB,IAAI,CAAC,WAAW,CAAC,EAAE;aAChB,OAAO,CAAC,wCAAwC,CAAC;aACjD,GAAG,CAAC,EAAE,CAAC,CAAC;IACb,CAAC;IAED;;;;;;;;OAQG;IACH,oBAAoB,CAAC,KAAa;QAChC,IAAI,CAAC,eAAe,EAAE,CAAC;QACvB,IAAI,CAAC,WAAW,CAAC,EAAE;aAChB,OAAO,CAAC,2CAA2C,CAAC;aACpD,GAAG,CAAC,GAAG,KAAK,KAAK,CAAC,CAAC;IACxB,CAAC;IAED,MAAM,CAAC,cAA4B,EAAE,QAAgB,EAAE;QACrD,IAAI,CAAC,eAAe,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,eAAe,CAAC,cAAc,CAAC,CAAC;QAC5C,OAAO,IAAI,CAAC,WAAW,CAAC,EAAE;aACvB,OAAO,CACN;;;;;KAKH,CACE;aACA,GAAG,CAAC,GAAG,EAAE,KAAK,CAAmB,CAAC;IACvC,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-hero-knowledge-index",
-  "version": "0.1.21",
+  "version": "0.1.24",
   "type": "module",
   "main": "dist/index.js",
   "bin": {
@@ -31,6 +31,7 @@
     "graphology-simple-path": "^0.2.0",
     "graphology-traversal": "^0.3.1",
     "graphology-types": "^0.24.8",
+    "ignore": "^5.3.2",
     "sqlite-vec": "^0.1.7-alpha.10",
     "yaml": "^2.7.0",
     "zod": "^3.25.0"

package/src/__tests__/config.test.ts

@@ -0,0 +1,173 @@
+import { describe, it, expect, beforeEach, afterEach, vi } from "vitest";
+import { mkdtempSync, writeFileSync, mkdirSync, existsSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir, homedir } from "node:os";
+import { loadConfig, expandHome, resolveConfigPath } from "../config.js";
+
+describe("expandHome", () => {
+  it("returns input unchanged when it does not start with ~", () => {
+    expect(expandHome("/absolute/path")).toBe("/absolute/path");
+    expect(expandHome("relative/path")).toBe("relative/path");
+    expect(expandHome("")).toBe("");
+  });
+
+  it("expands a lone ~", () => {
+    expect(expandHome("~")).toBe(homedir());
+  });
+
+  it("expands ~/ prefix to homedir/rest", () => {
+    expect(expandHome("~/thoughts")).toBe(join(homedir(), "thoughts"));
+    expect(expandHome("~/foo/bar")).toBe(join(homedir(), "foo/bar"));
+  });
+});
+
+describe("loadConfig", () => {
+  let originalEnv: string | undefined;
+  let tmpDir: string;
+
+  beforeEach(() => {
+    originalEnv = process.env.RALPH_KNOWLEDGE_CONFIG;
+    tmpDir = mkdtempSync(join(tmpdir(), "ralph-config-"));
+  });
+
+  afterEach(() => {
+    if (originalEnv === undefined) {
+      delete process.env.RALPH_KNOWLEDGE_CONFIG;
+    } else {
+      process.env.RALPH_KNOWLEDGE_CONFIG = originalEnv;
+    }
+    if (existsSync(tmpDir)) {
+      rmSync(tmpDir, { recursive: true, force: true });
+    }
+  });
+
+  it("returns {} when the config file is missing", () => {
+    // Point env var at a nonexistent path so we don't read the real ~/.ralph file.
+    process.env.RALPH_KNOWLEDGE_CONFIG = join(tmpDir, "nope.json");
+    expect(loadConfig()).toEqual({});
+  });
+
+  it("returns {} and warns on malformed JSON", () => {
+    const configPath = join(tmpDir, "broken.json");
+    writeFileSync(configPath, "{ not: valid json");
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const warn = vi.spyOn(console, "warn").mockImplementation(() => {});
+    const result = loadConfig();
+    expect(result).toEqual({});
+    expect(warn).toHaveBeenCalledTimes(1);
+    const msg = warn.mock.calls[0][0] as string;
+    expect(msg).toContain("Malformed JSON");
+    warn.mockRestore();
+  });
+
+  it("returns {} and warns when top-level is not an object", () => {
+    const configPath = join(tmpDir, "array.json");
+    writeFileSync(configPath, JSON.stringify(["not", "an", "object"]));
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const warn = vi.spyOn(console, "warn").mockImplementation(() => {});
+    expect(loadConfig()).toEqual({});
+    expect(warn).toHaveBeenCalledTimes(1);
+    warn.mockRestore();
+  });
+
+  it("expands ~ prefixes in roots[] to absolute paths", () => {
+    const configPath = join(tmpDir, "tilde.json");
+    writeFileSync(
+      configPath,
+      JSON.stringify({ roots: ["~/thoughts", "/absolute/dir"] }),
+    );
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const cfg = loadConfig();
+    expect(cfg.roots).toEqual([
+      join(homedir(), "thoughts"),
+      "/absolute/dir",
+    ]);
+  });
+
+  it("expands ~ in dbPath", () => {
+    const configPath = join(tmpDir, "db.json");
+    writeFileSync(
+      configPath,
+      JSON.stringify({ dbPath: "~/.ralph-hero/knowledge.db" }),
+    );
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const cfg = loadConfig();
+    expect(cfg.dbPath).toBe(join(homedir(), ".ralph-hero/knowledge.db"));
+  });
+
+  it("loads ignorePatterns as provided (no expansion)", () => {
+    const configPath = join(tmpDir, "ignore.json");
+    writeFileSync(
+      configPath,
+      JSON.stringify({ ignorePatterns: ["**/drafts/**", "*.bak"] }),
+    );
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const cfg = loadConfig();
+    expect(cfg.ignorePatterns).toEqual(["**/drafts/**", "*.bak"]);
+  });
+
+  it("honors RALPH_KNOWLEDGE_CONFIG env var override", () => {
+    const configPath = join(tmpDir, "override.json");
+    writeFileSync(
+      configPath,
+      JSON.stringify({ roots: ["/x"], ignorePatterns: ["y/**"], dbPath: "/z.db" }),
+    );
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const cfg = loadConfig();
+    expect(cfg).toEqual({
+      roots: ["/x"],
+      ignorePatterns: ["y/**"],
+      dbPath: "/z.db",
+    });
+  });
+
+  it("drops non-string roots and ignorePatterns entries", () => {
+    const configPath = join(tmpDir, "mixed.json");
+    writeFileSync(
+      configPath,
+      JSON.stringify({
+        roots: ["/a", 42, null, "/b"],
+        ignorePatterns: ["good", 7, "more"],
+      }),
+    );
+    process.env.RALPH_KNOWLEDGE_CONFIG = configPath;
+    const cfg = loadConfig();
+    expect(cfg.roots).toEqual(["/a", "/b"]);
+    expect(cfg.ignorePatterns).toEqual(["good", "more"]);
+  });
+});
+
+describe("resolveConfigPath", () => {
+  let originalEnv: string | undefined;
+
+  beforeEach(() => {
+    originalEnv = process.env.RALPH_KNOWLEDGE_CONFIG;
+  });
+
+  afterEach(() => {
+    if (originalEnv === undefined) {
+      delete process.env.RALPH_KNOWLEDGE_CONFIG;
+    } else {
+      process.env.RALPH_KNOWLEDGE_CONFIG = originalEnv;
+    }
+  });
+
+  it("defaults to ~/.ralph/knowledge.config.json when env var is unset", () => {
+    delete process.env.RALPH_KNOWLEDGE_CONFIG;
+    expect(resolveConfigPath()).toBe(
+      join(homedir(), ".ralph", "knowledge.config.json"),
+    );
+  });
+
+  it("expands ~ prefix in RALPH_KNOWLEDGE_CONFIG", () => {
+    process.env.RALPH_KNOWLEDGE_CONFIG = "~/custom/knowledge.json";
+    expect(resolveConfigPath()).toBe(
+      join(homedir(), "custom/knowledge.json"),
+    );
+  });
+
+  it("uses RALPH_KNOWLEDGE_CONFIG absolute path verbatim", () => {
+    process.env.RALPH_KNOWLEDGE_CONFIG = "/etc/ralph/knowledge.json";
+    expect(resolveConfigPath()).toBe("/etc/ralph/knowledge.json");
+  });
+});

package/src/__tests__/embedder.test.ts

@@ -1,5 +1,20 @@
-import { describe, it, expect } from "vitest";
-import { prepareTextForEmbedding } from "../embedder.js";
+import { describe, it, expect, vi, beforeEach } from "vitest";
+
+// Mock @huggingface/transformers so we don't need to load the real ONNX
+// model during unit tests. The fake pipeline returns a constant 384-dim
+// vector; we track call count via the `embedCalls` array below.
+const embedCalls: string[] = [];
+vi.mock("@huggingface/transformers", () => {
+  const fakePipeline = async (text: string, _opts: unknown) => {
+    embedCalls.push(text);
+    return { data: new Float32Array(384) };
+  };
+  return {
+    pipeline: vi.fn(async () => fakePipeline),
+  };
+});
+
+import { prepareTextForEmbedding, embedDocument } from "../embedder.js";
 
 describe("prepareTextForEmbedding", () => {
   it("includes title, tags, and first paragraph", () => {
@@ -40,14 +55,15 @@ describe("prepareTextForEmbedding", () => {
     expect(result).not.toContain("\n\n");
   });
 
-  it("truncates at MAX_CHARS (500) total", () => {
+  it("no longer truncates at 500 chars (MAX_CHARS removed)", () => {
     const longParagraph = "A".repeat(600);
     const result = prepareTextForEmbedding(
       "Title",
       ["tag1", "tag2"],
       longParagraph,
     );
-    expect(result.length).toBe(500);
+    // Title (5) + \n + tag1, tag2 (10) + \n + 600 A's = 617 chars
+    expect(result.length).toBe(617);
     expect(result.startsWith("Title\ntag1, tag2\n")).toBe(true);
   });
 
@@ -98,3 +114,86 @@ describe("prepareTextForEmbedding", () => {
     expect(result).toBe("My Title\ngraphology, search\nFirst paragraph.");
   });
 });
+
+describe("embedDocument", () => {
+  beforeEach(() => {
+    embedCalls.length = 0;
+  });
+
+  it("returns exactly one chunk for short content", async () => {
+    const result = await embedDocument("Title", ["tag"], "short content");
+    expect(result).toHaveLength(1);
+    expect(result[0]!.index).toBe(0);
+    expect(result[0]!.content).toBe("short content");
+    expect(result[0]!.charStart).toBe(0);
+    expect(result[0]!.charEnd).toBe("short content".length);
+    expect(result[0]!.embedding).toBeInstanceOf(Float32Array);
+  });
+
+  it("embeds with title + tagLine + chunk.content prepended", async () => {
+    await embedDocument("My Title", ["graphology", "search"], "body text");
+    expect(embedCalls).toHaveLength(1);
+    expect(embedCalls[0]).toBe("My Title\ngraphology, search\nbody text");
+  });
+
+  it("omits empty title/tags/content from the embed input", async () => {
+    await embedDocument("", [], "only content here");
+    expect(embedCalls).toContain("only content here");
+
+    embedCalls.length = 0;
+    await embedDocument("Just Title", [], "");
+    // Empty content -> one chunk with empty string, only title is non-empty.
+    expect(embedCalls).toContain("Just Title");
+  });
+
+  it("yields >= 4 chunks for an 8K-char document", async () => {
+    const longContent = "A".repeat(8000);
+    const result = await embedDocument("Title", [], longContent);
+    expect(result.length).toBeGreaterThanOrEqual(4);
+    // Each chunk gets its own embedding.
+    expect(embedCalls).toHaveLength(result.length);
+  });
+
+  it("produces Float32Array embeddings of length 384", async () => {
+    const result = await embedDocument("T", [], "hello world");
+    expect(result[0]!.embedding).toBeInstanceOf(Float32Array);
+    expect(result[0]!.embedding.length).toBe(384);
+  });
+
+  it("chunk indexes are monotonically increasing from 0", async () => {
+    const longContent = "word ".repeat(3000); // ~15K chars, many chunks
+    const result = await embedDocument("T", [], longContent);
+    expect(result.length).toBeGreaterThan(1);
+    for (let i = 0; i < result.length; i++) {
+      expect(result[i]!.index).toBe(i);
+    }
+  });
+
+  it("chunk offsets reconstruct the original content", async () => {
+    const content = "A".repeat(5000);
+    const result = await embedDocument("T", [], content);
+    for (const chunk of result) {
+      expect(content.slice(chunk.charStart, chunk.charEnd)).toBe(chunk.content);
+    }
+  });
+
+  it("empty content yields one chunk with empty content (anchors on title/tags)", async () => {
+    const result = await embedDocument("Just Title", ["some-tag"], "");
+    expect(result).toHaveLength(1);
+    expect(result[0]!.content).toBe("");
+    expect(result[0]!.charStart).toBe(0);
+    expect(result[0]!.charEnd).toBe(0);
+    // Still got embedded using title + tag.
+    expect(embedCalls).toContain("Just Title\nsome-tag");
+  });
+
+  it("respects custom chunker options", async () => {
+    const content = "A".repeat(500);
+    const result = await embedDocument("T", [], content, {
+      chunkSize: 100,
+      chunkOverlap: 10,
+    });
+    // With chunkSize=100 over 500 chars, we expect multiple chunks.
+    expect(result.length).toBeGreaterThan(1);
+  });
+});