ralph-hero-knowledge-index 0.1.29 → 0.1.31

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-knowledge",
-  "version": "0.1.29",
+  "version": "0.1.31",
   "description": "Knowledge graph for ralph-hero: semantic search, relationship traversal, and document indexing across thoughts/ documents. Optional companion to ralph-hero.",
   "author": {
     "name": "Chad Dubiel",

package/.mcp.json

@@ -2,7 +2,7 @@
   "mcpServers": {
     "ralph-knowledge": {
       "command": "npx",
-      "args": ["-y", "ralph-hero-knowledge-index@0.1.29"]
+      "args": ["-y", "ralph-hero-knowledge-index@0.1.31"]
     }
   }
 }

package/dist/chunker.js

@@ -127,6 +127,10 @@ function buildChunk(originalText, atoms, index) {
  * chunk ended at `prevEnd`. We walk backward through the atom list to find
  * the atom whose start >= prevEnd - chunkOverlap; that atom begins the
  * overlap region.
+ *
+ * NOTE: this function may return an index <= the previous chunk's first atom
+ * when the previous chunk consisted of a single atom shorter than chunkOverlap.
+ * The caller in chunkText clamps the result to ensure forward progress.
  */
 function findOverlapStartIndex(atoms, lastEndAtomIndex, prevEnd, chunkOverlap) {
     if (chunkOverlap <= 0) {
@@ -212,7 +216,14 @@ export function chunkText(text, opts = {}) {
         // Compute overlap start for the next chunk.
         const lastEndAtomIdx = j - 1;
         const nextStart = findOverlapStartIndex(atoms, lastEndAtomIdx, chunk.charEnd, chunkOverlap);
-        i = nextStart;
+        // Ensure forward progress: when a chunk consists of a single atom shorter
+        // than chunkOverlap, the overlap walk would land back on the same atom.
+        // Clamp to i + 1 in that case so we always advance, accepting that the
+        // resulting chunks will not overlap (this is the only correct option:
+        // overlap requires that the next chunk start within the previous chunk's
+        // span, but if the previous chunk has only one atom, there is no earlier
+        // position within its span to start from).
+        i = nextStart > i ? nextStart : i + 1;
     }
     return chunks;
 }

package/dist/chunker.js.map

@@ -1 +1 @@
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package/dist/embedder.js

@@ -16,7 +16,19 @@ export async function embed(text) {
         pooling: "mean",
         normalize: true,
     });
-    return new Float32Array(output.data);
+    // Copy data into a freshly allocated Float32Array (constructor's ArrayLike
+    // overload iterates and assigns, decoupling from the source buffer).
+    const embedding = new Float32Array(output.data);
+    // GH-911: eagerly release the underlying ONNX-runtime native tensor buffer.
+    // V8 cannot reclaim native (off-heap) memory fast enough across the per-chunk
+    // await loop in `embedDocument()`, which causes the corpus reindex to OOM at
+    // ~150 chunks. `Tensor.dispose()` (transformers.js v3) calls
+    // `ort_tensor.dispose()` which frees the native buffer immediately.
+    // The guard tolerates test mocks that lack a `dispose` method.
+    if (output && typeof output.dispose === "function") {
+        output.dispose();
+    }
+    return embedding;
 }
 /**
  * Embed a document by splitting it into chunks and emitting one embedding

package/dist/embedder.js.map

@@ -1 +1 @@
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package/dist/reindex.js

@@ -101,7 +101,15 @@ export async function reindex(dirs, dbPath, generate = false, ignorePatterns) {
             : filePath;
         const id = basename(filePath, ".md");
         const parsed = parseDocument(id, relPath, raw);
-        parsedDocs.push(parsed);
+        // GH-911: only accumulate parsed docs when `generate=true` (the rare case
+        // where `generateIndexes()` runs at the end of the loop). On the live
+        // corpus this avoids pinning every parsed document's content + relationships
+        // for the whole run; under `generate=false` (the default CLI path), the
+        // accumulator is skipped entirely so V8 can reclaim each parsed document
+        // immediately after its DB rows are written.
+        if (generate) {
+            parsedDocs.push(parsed);
+        }
         const missing = [];
         if (!parsed.date)
             missing.push("date");

package/dist/reindex.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-hero-knowledge-index",
-  "version": "0.1.29",
+  "version": "0.1.31",
   "type": "module",
   "main": "dist/index.js",
   "bin": {

package/src/__tests__/chunker.test.ts

@@ -244,3 +244,59 @@ describe("chunkText — separator priority", () => {
     expect(lastEnd).toBe(text.length);
   });
 });
+
+describe("chunkText — forward progress invariant", () => {
+  // Regression test for GH-916. Pre-fix this OOMs.
+  it("terminates when a chunk would consist of a single atom shorter than chunkOverlap", () => {
+    // Trigger: atom N is short (< 256 chars), atom N+1 is large enough that
+    // packing them together would exceed chunkSize (2048).
+    const shortAtom = "short paragraph that is under 256 chars.\n\n";
+    const longAtom = "x".repeat(1900) + "\n\n";
+    const text = shortAtom + longAtom + "tail.";
+    const chunks = chunkText(text);
+    // We don't care about the exact count; we care that chunkText returns at
+    // all (pre-fix it loops forever) and that all chunks have non-empty content.
+    expect(chunks.length).toBeGreaterThan(0);
+    expect(chunks.length).toBeLessThan(100); // sanity: no runaway
+    for (const c of chunks) {
+      expect(c.content.length).toBeGreaterThan(0);
+    }
+  });
+
+  it("makes strict forward progress: chunk[i+1].charStart > chunk[i].charStart", () => {
+    // Build an input that triggers many single-atom chunks.
+    const blocks = [];
+    for (let i = 0; i < 20; i++) {
+      blocks.push("short " + i + ".\n\n");
+      blocks.push("x".repeat(1900) + "\n\n");
+    }
+    const chunks = chunkText(blocks.join(""));
+    expect(chunks.length).toBeGreaterThan(0);
+    for (let i = 1; i < chunks.length; i++) {
+      expect(chunks[i]!.charStart).toBeGreaterThan(chunks[i - 1]!.charStart);
+    }
+  });
+
+  it("chunks the GH-916 fixture file in bounded time and memory", () => {
+    // Path-independent fixture: a markdown sample that mirrors the trigger
+    // pattern (short paragraphs interspersed with large code blocks).
+    const sample = [
+      "# Heading\n\n",
+      "Short intro paragraph.\n\n",
+      "```python\n" + "code line\n".repeat(180) + "```\n\n",
+      "Short follow-up.\n\n",
+      "```python\n" + "more code\n".repeat(180) + "```\n\n",
+      "End.",
+    ].join("");
+    const start = Date.now();
+    const chunks = chunkText(sample);
+    const elapsed = Date.now() - start;
+    expect(elapsed).toBeLessThan(1000); // pre-fix this would not return
+    expect(chunks.length).toBeGreaterThan(0);
+    expect(chunks.length).toBeLessThan(50); // sanity: no runaway
+    // Spot-check the canonical invariant
+    for (const c of chunks) {
+      expect(sample.slice(c.charStart, c.charEnd)).toBe(c.content);
+    }
+  });
+});

package/src/__tests__/embedder.test.ts

@@ -3,18 +3,26 @@ 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.
+//
+// GH-911: the mock now also exposes a `dispose` mock on each output so we can
+// assert that `embed()` releases the native tensor buffer eagerly. The dispose
+// invocations are aggregated on the module-level `disposeCalls` array so tests
+// can introspect call counts across multiple `embed()` invocations.
 const embedCalls: string[] = [];
+const disposeCalls: ReturnType<typeof vi.fn>[] = [];
 vi.mock("@huggingface/transformers", () => {
   const fakePipeline = async (text: string, _opts: unknown) => {
     embedCalls.push(text);
-    return { data: new Float32Array(384) };
+    const dispose = vi.fn();
+    disposeCalls.push(dispose);
+    return { data: new Float32Array(384), dispose };
   };
   return {
     pipeline: vi.fn(async () => fakePipeline),
   };
 });
 
-import { prepareTextForEmbedding, embedDocument } from "../embedder.js";
+import { prepareTextForEmbedding, embed, embedDocument } from "../embedder.js";
 import type { LlmClient } from "../llm-client.js";
 
 function makeMockLlm(contextualize: LlmClient["contextualize"]): LlmClient {
@@ -123,6 +131,47 @@ describe("prepareTextForEmbedding", () => {
   });
 });
 
+// GH-911: regression tests for tensor disposal in embed(). The mock exposes a
+// vi.fn() on each output's `dispose` slot; embed() must invoke it once per
+// call so the underlying ONNX-runtime native buffer is freed eagerly instead
+// of waiting on V8 GC (which cannot keep up with the per-chunk await loop).
+describe("embed (tensor disposal)", () => {
+  beforeEach(() => {
+    embedCalls.length = 0;
+    disposeCalls.length = 0;
+  });
+
+  it("calls output.dispose() exactly once per embed() invocation", async () => {
+    const result = await embed("hello");
+    expect(result).toBeInstanceOf(Float32Array);
+    expect(result.length).toBe(384);
+    expect(disposeCalls).toHaveLength(1);
+    expect(disposeCalls[0]).toHaveBeenCalledTimes(1);
+  });
+
+  it("calls dispose on every output across multiple invocations", async () => {
+    await embed("first");
+    await embed("second");
+    await embed("third");
+    expect(disposeCalls).toHaveLength(3);
+    for (const dispose of disposeCalls) {
+      expect(dispose).toHaveBeenCalledTimes(1);
+    }
+  });
+
+  it("returns a Float32Array independent of the source tensor (data is copied before dispose)", async () => {
+    const result = await embed("text");
+    // dispose was called, but the returned Float32Array is still usable —
+    // verifies the data was copied (not aliased) before disposal.
+    expect(disposeCalls[0]).toHaveBeenCalledTimes(1);
+    expect(() => {
+      result[0] = 1.0;
+      void result[0];
+    }).not.toThrow();
+    expect(result.length).toBe(384);
+  });
+});
+
 describe("embedDocument", () => {
   beforeEach(() => {
     embedCalls.length = 0;

package/src/__tests__/reindex.test.ts

@@ -67,6 +67,22 @@ vi.mock("../llm-client.js", () => ({
   })),
 }));
 
+// GH-911: mock generateIndexes so we can assert the parsedDocs[] accumulator
+// gate. When generate=false (the default CLI path), the accumulator is skipped
+// entirely and generateIndexes is not called. When generate=true, the
+// accumulator is populated and generateIndexes is invoked with a non-empty
+// ParsedDocument[].
+//
+// `vi.hoisted()` is required because `vi.mock` factory bodies are hoisted to
+// the top of the file before regular `const` declarations run. Hoisting the
+// mock fn keeps it accessible from both the factory and the test body.
+const { mockGenerateIndexes } = vi.hoisted(() => ({
+  mockGenerateIndexes: vi.fn(),
+}));
+vi.mock("../generate-indexes.js", () => ({
+  generateIndexes: mockGenerateIndexes,
+}));
+
 import { embedDocument } from "../embedder.js";
 import { reindex } from "../reindex.js";
 import { KnowledgeDB } from "../db.js";
@@ -120,6 +136,8 @@ describe("incremental reindex", () => {
     mockLlmAvailable.mockResolvedValue(true);
     mockLlmContextualize.mockReset();
     mockLlmContextualize.mockResolvedValue("");
+    // Reset the GH-911 generateIndexes mock so per-test call counts are clean.
+    mockGenerateIndexes.mockClear();
     // Default the flag to disabled for legacy tests so the existing 17 scenarios
     // don't accidentally call the mocked LLM — the Phase 6 tests opt back in
     // explicitly via `process.env.RALPH_CONTEXTUAL_RETRIEVAL = "1"`.
@@ -812,4 +830,60 @@ describe("incremental reindex", () => {
       db.close();
     }
   });
+
+  // ---- GH-911: parsedDocs[] accumulator gating ----
+  //
+  // The accumulator is only consumed by `generateIndexes()` when `generate=true`.
+  // Phase 2 wraps `parsedDocs.push(parsed)` in `if (generate)` so the
+  // unbounded array isn't built up under the default `generate=false` CLI path.
+  // These tests exercise both branches via the mocked `generateIndexes`.
+
+  it("scenario 28: generate=false skips generateIndexes entirely", async () => {
+    writeFileSync(join(dir, "doc-a.md"), makeDoc("Doc A"));
+    writeFileSync(join(dir, "doc-b.md"), makeDoc("Doc B"));
+
+    // Default generate=false (third positional arg omitted).
+    await reindex([dir], dbPath);
+
+    expect(mockGenerateIndexes).not.toHaveBeenCalled();
+  });
+
+  it("scenario 29: generate=true invokes generateIndexes with a non-empty ParsedDocument[]", async () => {
+    writeFileSync(join(dir, "doc-a.md"), makeDoc("Doc A"));
+    writeFileSync(join(dir, "doc-b.md"), makeDoc("Doc B"));
+
+    await reindex([dir], dbPath, true);
+
+    expect(mockGenerateIndexes).toHaveBeenCalledTimes(1);
+    const callArgs = mockGenerateIndexes.mock.calls[0];
+    // First arg: outDir (the first directory passed to reindex).
+    expect(callArgs[0]).toBe(dir);
+    // Second arg: ParsedDocument[] populated with both docs.
+    const parsedDocs = callArgs[1] as Array<{ id: string }>;
+    expect(parsedDocs).toHaveLength(2);
+    const ids = parsedDocs.map((d) => d.id).sort();
+    expect(ids).toEqual(["doc-a", "doc-b"]);
+  });
+
+  it("scenario 30: generate=false produces same DB state as generate=true (only the index files differ)", async () => {
+    writeFileSync(join(dir, "doc-a.md"), makeDoc("Doc A"));
+    writeFileSync(join(dir, "doc-b.md"), makeDoc("Doc B"));
+
+    await reindex([dir], dbPath, false);
+
+    const db = new KnowledgeDB(dbPath);
+    try {
+      expect(db.getDocument("doc-a")).toBeTruthy();
+      expect(db.getDocument("doc-b")).toBeTruthy();
+      // Embedding rows should be present even though the accumulator was skipped.
+      const chunkCount = (db.db
+        .prepare("SELECT COUNT(*) as n FROM chunks")
+        .get() as { n: number }).n;
+      expect(chunkCount).toBeGreaterThanOrEqual(2);
+    } finally {
+      db.close();
+    }
+    // generateIndexes was correctly skipped under the false path.
+    expect(mockGenerateIndexes).not.toHaveBeenCalled();
+  });
 });

package/src/chunker.ts

@@ -167,6 +167,10 @@ function buildChunk(
  * chunk ended at `prevEnd`. We walk backward through the atom list to find
  * the atom whose start >= prevEnd - chunkOverlap; that atom begins the
  * overlap region.
+ *
+ * NOTE: this function may return an index <= the previous chunk's first atom
+ * when the previous chunk consisted of a single atom shorter than chunkOverlap.
+ * The caller in chunkText clamps the result to ensure forward progress.
  */
 function findOverlapStartIndex(
   atoms: Piece[],
@@ -272,7 +276,14 @@ export function chunkText(text: string, opts: ChunkerOptions = {}): Chunk[] {
       chunk.charEnd,
       chunkOverlap,
     );
-    i = nextStart;
+    // Ensure forward progress: when a chunk consists of a single atom shorter
+    // than chunkOverlap, the overlap walk would land back on the same atom.
+    // Clamp to i + 1 in that case so we always advance, accepting that the
+    // resulting chunks will not overlap (this is the only correct option:
+    // overlap requires that the next chunk start within the previous chunk's
+    // span, but if the previous chunk has only one atom, there is no earlier
+    // position within its span to start from).
+    i = nextStart > i ? nextStart : i + 1;
   }
 
   return chunks;

package/src/embedder.ts

@@ -27,7 +27,19 @@ export async function embed(text: string): Promise<Float32Array> {
     pooling: "mean",
     normalize: true,
   });
-  return new Float32Array(output.data as ArrayLike<number>);
+  // Copy data into a freshly allocated Float32Array (constructor's ArrayLike
+  // overload iterates and assigns, decoupling from the source buffer).
+  const embedding = new Float32Array(output.data as ArrayLike<number>);
+  // GH-911: eagerly release the underlying ONNX-runtime native tensor buffer.
+  // V8 cannot reclaim native (off-heap) memory fast enough across the per-chunk
+  // await loop in `embedDocument()`, which causes the corpus reindex to OOM at
+  // ~150 chunks. `Tensor.dispose()` (transformers.js v3) calls
+  // `ort_tensor.dispose()` which frees the native buffer immediately.
+  // The guard tolerates test mocks that lack a `dispose` method.
+  if (output && typeof (output as { dispose?: unknown }).dispose === "function") {
+    (output as { dispose: () => void }).dispose();
+  }
+  return embedding;
 }
 
 /**

package/src/reindex.ts

@@ -117,7 +117,15 @@ export async function reindex(
     const id = basename(filePath, ".md");
 
     const parsed = parseDocument(id, relPath, raw);
-    parsedDocs.push(parsed);
+    // GH-911: only accumulate parsed docs when `generate=true` (the rare case
+    // where `generateIndexes()` runs at the end of the loop). On the live
+    // corpus this avoids pinning every parsed document's content + relationships
+    // for the whole run; under `generate=false` (the default CLI path), the
+    // accumulator is skipped entirely so V8 can reclaim each parsed document
+    // immediately after its DB rows are written.
+    if (generate) {
+      parsedDocs.push(parsed);
+    }
 
     const missing: string[] = [];
     if (!parsed.date) missing.push("date");