fix(chunker): estimated-token hard cap — URL-dense/CJK-fallback chunks overflow strict embedding-server token limits

Takeover of #2847 (rebased onto current master). Fixes #2826.

- cjk.ts: estimateEmbeddingTokens() — conservative per-char-class token
  estimate (CJK 1.0, other 0.75, whitespace 0.1 per code unit).
- recursive.ts (MARKDOWN_CHUNKER_VERSION 3→4): countWords floored at
  ceil(nonWhitespaceChars/6); capByEstimatedTokens() final pass with
  ChunkOptions.maxTokens (default 1500).
- code.ts (CHUNKER_VERSION 4→5): capCodeChunks() applies the same cap to
  AST-path chunks that splitLargeNode can't subdivide.

Co-authored-by: paul-0320 <paul-0320@users.noreply.github.com>

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/tutorials/company-brain.md

@@ -223,16 +223,14 @@ export GBRAIN_REMOTE_CLIENT_ID=<Alice's client_id>
 export GBRAIN_REMOTE_CLIENT_SECRET=<Alice's client_secret>
 export GBRAIN_REMOTE_MCP_URL=https://brain.acme-co.com/mcp
 
-gbrain search "performance review"
+gbrain search "performance review" --remote
 ```
 
-(On a thin-client install every shared op routes through the remote MCP server automatically — no flag needed. The env vars select whose credentials the call uses.)
-
 Alice should see results only from `customers` and `shared`. The performance-review notes live in `internal`, which she's not scoped to read. She shouldn't see them.
 
 ```bash
 # Terminal 2, as Bob (export his credentials similarly)
-gbrain search "performance review"
+gbrain search "performance review" --remote
 ```
 
 Bob should see the performance-review notes from `internal`, plus anything related from `shared`. He shouldn't see anything that lives only in `customers`.
@@ -516,7 +514,7 @@ The first sync embeds every page, which takes time. Check `gbrain sources status
 
 ### "I see a page I shouldn't see"
 
-This shouldn't happen, but if you suspect it, run `gbrain search <query> --json` as the constrained client (thin-client install, with the client's `GBRAIN_REMOTE_*` env exported) and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
+This shouldn't happen, but if you suspect it, run `gbrain search <query> --remote --json` as the constrained client and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
 
 ### "The synthesized answer is wrong"
 

src/cli.ts

@@ -464,11 +464,7 @@ async function main() {
     // routed path. Date → ISO string; bigint → string (postgres.js shape);
     // Buffer → object. Microsecond-cost; eliminates a whole drift bug class.
     const result = JSON.parse(JSON.stringify(rawResult, bigintToStringReplacer));
-    // #380 pass-through: `--json` (undeclared on most ops, promised by docs)
-    // emits the raw op result instead of the human formatter.
-    const output = params.json === true
-      ? JSON.stringify(result, null, 2) + '\n'
-      : formatResult(op.name, result);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     // v0.42.20.0 (codex D4): on error, set exitCode + return so the `finally`
@@ -551,10 +547,7 @@ async function runThinClientRouted(
       signal: sigintController.signal,
     });
     const result = unpackToolResult(raw);
-    // #380: same --json seam as the local-engine path (renderer parity).
-    const output = params.json === true
-      ? JSON.stringify(result, null, 2) + '\n'
-      : formatResult(op.name, result);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     if (e instanceof RemoteMcpError) {
@@ -764,28 +757,10 @@ export function resolveQueryImage(
   return { path: imagePath, base64, mime };
 }
 
-/**
- * #380: undeclared flags that are honored DOWNSTREAM of parseOpArgs and must
- * keep passing through when unknown flags become hard errors:
- *   - source     → makeContext's resolveSourceId (the --source axis)
- *   - brain      → the mount/brain routing axis (docs promise the flag)
- *   - dry_run    → makeContext's ctx.dryRun (ops without a declared dry_run)
- *   - json       → raw-JSON output seam (local + thin-client paths)
- */
-const PASSTHROUGH_VALUE_FLAGS = new Set(['source', 'brain']);
-const PASSTHROUGH_BOOL_FLAGS = new Set(['dry_run', 'json']);
-
 export function parseOpArgs(op: Operation, args: string[]): Record<string, unknown> {
   const params: Record<string, unknown> = {};
   const positional = op.cliHints?.positional || [];
   let posIdx = 0;
-  const cliName = op.cliHints?.name || op.name;
-  const MAX_STDIN = 5_000_000; // 5MB cap, shared by stdin and --file
-  // #380: `--file <path>` fills the op's declared stdin param (put's `content`)
-  // from a file. Driven by cliHints.stdin — no per-op hard-coding — and
-  // disabled when the op declares a real `file` param of its own.
-  const fileParam = op.cliHints?.stdin && !op.params.file ? op.cliHints.stdin : undefined;
-  let filePath: string | undefined;
 
   for (let i = 0; i < args.length; i++) {
     const arg = args[i];
@@ -799,42 +774,12 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
         }
       }
       const key = arg.slice(2).replace(/-/g, '_');
-      if (fileParam && key === 'file') {
-        if (i + 1 >= args.length) {
-          console.error(`Error: ${arg} requires a value.`);
-          process.exit(1);
-        }
-        filePath = args[++i];
-        continue;
-      }
       const paramDef = op.params[key];
-      if (!paramDef) {
-        if (PASSTHROUGH_BOOL_FLAGS.has(key)) {
-          params[key] = true;
-          continue;
-        }
-        if (PASSTHROUGH_VALUE_FLAGS.has(key)) {
-          if (i + 1 >= args.length) {
-            console.error(`Error: ${arg} requires a value.`);
-            process.exit(1);
-          }
-          params[key] = args[++i];
-          continue;
-        }
-        // #380: unknown flags were silently swallowed into params, so typos
-        // like `put --file` created empty pages instead of erroring.
-        console.error(`Unknown option for gbrain ${cliName}: ${arg}`);
-        console.error(`Run 'gbrain ${cliName} --help' for valid flags.`);
-        process.exit(1);
-      }
-      if (paramDef.type === 'boolean') {
+      if (paramDef?.type === 'boolean') {
         params[key] = true;
       } else if (i + 1 < args.length) {
         params[key] = args[++i];
-        if (paramDef.type === 'number') params[key] = Number(params[key]);
-      } else {
-        console.error(`Error: ${arg} requires a value.`);
-        process.exit(1);
+        if (paramDef?.type === 'number') params[key] = Number(params[key]);
       }
     } else if (posIdx < positional.length) {
       const key = positional[posIdx++];
@@ -843,30 +788,10 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
     }
   }
 
-  // #380: resolve --file AFTER the loop so --file/--content conflicts are
-  // caught in either order.
-  if (filePath !== undefined && fileParam) {
-    if (params[fileParam] !== undefined) {
-      console.error(`Error: use only one of --file, --${fileParam}, or stdin for gbrain ${cliName}.`);
-      process.exit(1);
-    }
-    let fileContent: string;
-    try {
-      fileContent = readFileSync(filePath, 'utf-8');
-    } catch (e) {
-      console.error(`Error: cannot read --file ${filePath}: ${e instanceof Error ? e.message : String(e)}`);
-      process.exit(1);
-    }
-    if (Buffer.byteLength(fileContent, 'utf-8') > MAX_STDIN) {
-      console.error(`Error: file content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
-      process.exit(1);
-    }
-    params[fileParam] = fileContent;
-  }
-
   // Read stdin for content params
   if (op.cliHints?.stdin && !params[op.cliHints.stdin] && !process.stdin.isTTY) {
     const stdinContent = readFileSync(0, 'utf-8');
+    const MAX_STDIN = 5_000_000; // 5MB
     if (Buffer.byteLength(stdinContent, 'utf-8') > MAX_STDIN) {
       console.error(`Error: stdin content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
@@ -2328,10 +2253,6 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${key}>` : `  --${key.replace(/_/g, '-')}`;
       console.log(`${prefix.padEnd(28)} ${def.description || ''}${req}`);
     }
-    // #380: ops that read stdin also accept --file <path> (parseOpArgs).
-    if (op.cliHints?.stdin && !op.params.file) {
-      console.log(`${'  --file <path>'.padEnd(28)} Read ${op.cliHints.stdin} from a file (alternative to --${op.cliHints.stdin} or stdin)`);
-    }
   }
 }
 

src/core/chunkers/code.ts

@@ -18,8 +18,9 @@
  * at runtime.
  */
 
-import { chunkText as recursiveChunk } from './recursive.ts';
+import { chunkText as recursiveChunk, capByEstimatedTokens, DEFAULT_MAX_EST_TOKENS } from './recursive.ts';
 import { buildQualifiedName } from './qualified-names.ts';
+import { estimateEmbeddingTokens } from '../cjk.ts';
 
 // Embed the tree-sitter runtime + per-language grammars as files.
 // `with { type: 'file' }` returns a path (string) at runtime. Bun bundles
@@ -111,7 +112,15 @@ import G_ZIG from '../../assets/wasm/grammars/tree-sitter-zig.wasm' with { type:
 // chunks get the new columns populated. Without this, the v28 backfill
 // gives every existing chunk a search_vector but subsequent Layer 5 AST
 // work would silently no-op.
-export const CHUNKER_VERSION = 4;
+//
+// v5: estimated-token hard cap on AST-path chunks (capCodeChunks). A node
+// splitLargeNode can't subdivide (giant single-statement function, huge
+// literal) previously shipped WHOLE regardless of size and could overflow
+// strict per-request embedding-token limits (local llama-server crashes
+// past ~2,050 tokens, measured). Mirrors the markdown
+// chunker's v4 cap; fallback-path chunks are already capped inside
+// recursiveChunk.
+export const CHUNKER_VERSION = 5;
 
 // Lazy-loaded tree-sitter module (v0.22.x API: Parser is default export)
 let Parser: typeof import('web-tree-sitter') | null = null;
@@ -708,7 +717,7 @@ export async function chunkCodeTextFull(
     if (chunks.length === 0) {
       return { chunks: fallbackChunks(source, filePath, language, opts), edges: rawEdges };
     }
-    return { chunks: mergeSmallSiblings(chunks, chunkTarget), edges: rawEdges };
+    return { chunks: capCodeChunks(mergeSmallSiblings(chunks, chunkTarget)), edges: rawEdges };
   } catch {
     return { chunks: fallbackChunks(source, filePath, language, opts), edges: [] };
   } finally {
@@ -791,6 +800,33 @@ function mergeSmallSiblings(chunks: CodeChunk[], chunkTarget: number): CodeChunk
   return merged;
 }
 
+/**
+ * v5 final safety pass for AST-path chunks: split any chunk whose
+ * ESTIMATED embedding tokens (conservative per-char-class heuristic,
+ * cjk.ts) exceed DEFAULT_MAX_EST_TOKENS. Reaches chunks the AST logic
+ * can't subdivide — splitLargeNode returns [] for nodes with < 2 body
+ * children (giant single-statement functions, huge literals), which
+ * previously shipped whole at any size.
+ *
+ * Split pieces inherit the source chunk's metadata verbatim; start/end
+ * lines become approximate for pieces after the first. Acceptable —
+ * these chunks exist for embedding + retrieval, and the alternative was
+ * an embedding request the server rejects (or worse, crashes on).
+ */
+function capCodeChunks(chunks: CodeChunk[]): CodeChunk[] {
+  if (chunks.every((c) => estimateEmbeddingTokens(c.text) <= DEFAULT_MAX_EST_TOKENS)) {
+    return chunks;
+  }
+  const out: CodeChunk[] = [];
+  for (const c of chunks) {
+    const pieces = capByEstimatedTokens(c.text, DEFAULT_MAX_EST_TOKENS);
+    for (const piece of pieces) {
+      out.push({ ...c, text: piece, index: out.length, metadata: { ...c.metadata } });
+    }
+  }
+  return out;
+}
+
 function buildMergedChunk(group: CodeChunk[], index: number): CodeChunk {
   const first = group[0]!;
   const last = group[group.length - 1]!;

src/core/chunkers/recursive.ts

@@ -17,7 +17,13 @@
  * Lossless invariant: non-overlapping portions reassemble to original.
  */
 
-import { countCJKAwareWords, CJK_SENTENCE_DELIMITERS, CJK_CLAUSE_DELIMITERS } from '../cjk.ts';
+import {
+  countCJKAwareWords,
+  CJK_SENTENCE_DELIMITERS,
+  CJK_CLAUSE_DELIMITERS,
+  charEmbedTokenWeight,
+  estimateEmbeddingTokens,
+} from '../cjk.ts';
 
 /**
  * Markdown chunker version. Folded into the per-page chunker_version column
@@ -33,8 +39,20 @@ import { countCJKAwareWords, CJK_SENTENCE_DELIMITERS, CJK_CLAUSE_DELIMITERS } fr
  * re-embed (not re-chunk) so existing pages pick up the wrapper on the
  * post-upgrade reembed sweep. See
  * `src/core/contextual-retrieval-service.ts`.
+ *
+ * v4: estimated-token hard cap + whitespace-word undercount fix. The word
+ * pipeline counted a 150-char URL as ONE whitespace word, so URL/phone/
+ * email-dense docs (CJK density < 0.30 → whitespace fallback) produced
+ * 3-4K-char chunks that overflow strict per-request embedding-token
+ * limits (measured: local llama-server crashes past ~2,050 tokens; URL
+ * soup tokenizes at ~1.6 chars/token). Two changes:
+ *   1. countWords() floors the count at ceil(nonWhitespaceChars/6) so a
+ *      URL counts roughly per-character, not as one word.
+ *   2. capByEstimatedTokens() final pass guarantees every chunk fits
+ *      `maxTokens` (default 1500) under a conservative per-char-class
+ *      token estimate, regardless of how word counting misjudged it.
  */
-export const MARKDOWN_CHUNKER_VERSION = 3;
+export const MARKDOWN_CHUNKER_VERSION = 4;
 
 const DELIMITERS: string[][] = [
   ['\n\n'],                          // L0: paragraphs
@@ -48,8 +66,20 @@ export interface ChunkOptions {
   chunkSize?: number;    // target words per chunk (default 300)
   chunkOverlap?: number; // overlap words (default 50)
   maxChars?: number;     // hard cap on any chunk's char length (default 6000)
+  /**
+   * v4: hard cap on any chunk's ESTIMATED embedding tokens (default 1500).
+   * Estimate = conservative per-char-class weights (see cjk.ts
+   * estimateEmbeddingTokens) — deliberately high, so the real tokenizer
+   * count stays below this value. Default leaves headroom for the
+   * contextual-retrieval wrapper (≤ ~630 chars) under a ~2,050-token
+   * per-request embedding server limit.
+   */
+  maxTokens?: number;
 }
 
+/** v4 default for ChunkOptions.maxTokens — see the field doc above. */
+export const DEFAULT_MAX_EST_TOKENS = 1500;
+
 export interface TextChunk {
   text: string;
   index: number;
@@ -73,6 +103,7 @@ export function chunkText(text: string, opts?: ChunkOptions): TextChunk[] {
   const chunkSize = opts?.chunkSize || 300;
   const chunkOverlap = opts?.chunkOverlap || 50;
   const maxChars = opts?.maxChars || 6000;
+  const maxTokens = opts?.maxTokens || DEFAULT_MAX_EST_TOKENS;
 
   if (!text || text.trim().length === 0) return [];
 
@@ -89,8 +120,9 @@ export function chunkText(text: string, opts?: ChunkOptions): TextChunk[] {
 
   const wordCount = countWords(stripped);
   if (wordCount <= chunkSize) {
-    // Single-chunk path: still apply the maxChars cap.
-    const capped = capByChars(stripped.trim(), maxChars);
+    // Single-chunk path: still apply the maxChars + maxTokens caps.
+    const capped = capByChars(stripped.trim(), maxChars)
+      .flatMap((t) => capByEstimatedTokens(t, maxTokens));
     return capped.map((t, i) => ({ text: t, index: i }));
   }
 
@@ -101,9 +133,14 @@ export function chunkText(text: string, opts?: ChunkOptions): TextChunk[] {
   // v0.32.7: hard char cap. Catches pathological CJK + whitespace-less text
   // that the word-level pipeline can't bound (a single Chinese paragraph can
   // exceed 8192 OpenAI embedding tokens at any word count).
+  // v4: estimated-token cap on top — the char cap alone passes token-dense
+  // content (URL soup at ~1.6 chars/token) that overflows strict embedding
+  // server limits.
   const capped: string[] = [];
   for (const chunk of withOverlap) {
-    capped.push(...capByChars(chunk.trim(), maxChars));
+    for (const piece of capByChars(chunk.trim(), maxChars)) {
+      capped.push(...capByEstimatedTokens(piece, maxTokens));
+    }
   }
   return capped.map((t, i) => ({ text: t, index: i }));
 }
@@ -132,6 +169,68 @@ function capByChars(text: string, maxChars: number): string[] {
   return out;
 }
 
+/**
+ * How far back (in chars) the token cap looks for a friendly cut point
+ * before falling back to a hard cut. 300 covers typical rollup/list line
+ * lengths so forced splits land at line starts, not mid-URL.
+ */
+const TOKEN_CAP_CUT_LOOKBACK = 300;
+
+/**
+ * v4: hard-cap a chunk's ESTIMATED embedding tokens. Final safety pass —
+ * runs after capByChars on every chunk, so no upstream miscounting
+ * (whitespace-word fallback, overlap inflation, char-cap survivors) can
+ * emit a chunk past `maxTokens`.
+ *
+ * Cut placement prefers, within the last TOKEN_CAP_CUT_LOOKBACK chars of
+ * the window: a newline, then any whitespace, then a hard cut. This keeps
+ * forced splits off mid-line/mid-URL positions for list-shaped content
+ * and inside code fences. No overlap is added (pieces stay lossless
+ * modulo the trims the char cap already applies).
+ *
+ * @internal exported for the code chunker (code.ts) and tests.
+ */
+export function capByEstimatedTokens(text: string, maxTokens: number): string[] {
+  if (text.length === 0) return [];
+  if (estimateEmbeddingTokens(text) <= maxTokens) return [text];
+
+  const out: string[] = [];
+  let start = 0;
+  while (start < text.length) {
+    // Greedily extend the window until the next char would break the cap.
+    // Always take at least one char so the loop makes forward progress.
+    let est = 0;
+    let end = start;
+    while (end < text.length) {
+      const w = charEmbedTokenWeight(text.charCodeAt(end));
+      if (est + w > maxTokens && end > start) break;
+      est += w;
+      end++;
+    }
+
+    if (end < text.length) {
+      const windowStart = Math.max(start + 1, end - TOKEN_CAP_CUT_LOOKBACK);
+      let cut = text.lastIndexOf('\n', end - 1);
+      if (cut < windowStart) {
+        cut = -1;
+        for (let i = end - 1; i >= windowStart; i--) {
+          const code = text.charCodeAt(i);
+          if (code === 0x20 || (code >= 0x09 && code <= 0x0d)) {
+            cut = i;
+            break;
+          }
+        }
+      }
+      if (cut >= windowStart) end = cut + 1;
+    }
+
+    const slice = text.slice(start, end).trim();
+    if (slice.length > 0) out.push(slice);
+    start = end;
+  }
+  return out;
+}
+
 function recursiveSplit(text: string, level: number, target: number): string[] {
   if (level >= DELIMITERS.length) {
     // Level 4: split on whitespace
@@ -317,7 +416,19 @@ function extractTrailingContext(text: string, targetWords: number): string {
  * Delegated to src/core/cjk.ts so the slugify whitelist, expansion
  * detection, and PGLite keyword fallback all agree on what "CJK enough"
  * means.
+ *
+ * v4: floored at ceil(nonWhitespaceChars/6). The whitespace fallback
+ * counts a 150-char URL as ONE word, so URL/phone/email-dense docs
+ * (whose ASCII mass pushes CJK density below the 0.30 threshold) were
+ * sized at a fraction of their real bulk and merged into 3-4K-char
+ * chunks. The floor makes long whitespace-less runs count roughly
+ * per-character while leaving normal Latin prose untouched (average
+ * English word ≈ 5 chars < 6, so the whitespace count still wins).
+ * Kept local to the chunker — search/expansion.ts keeps the original
+ * countCJKAwareWords semantics for its query-length check.
  */
 function countWords(text: string): number {
-  return countCJKAwareWords(text);
+  const cjkAware = countCJKAwareWords(text);
+  const nonWhitespace = text.replace(/\s/g, '').length;
+  return Math.max(cjkAware, Math.ceil(nonWhitespace / 6));
 }

src/core/cjk.ts

@@ -65,3 +65,64 @@ export function countCJKAwareWords(s: string): number {
 export function escapeLikePattern(s: string): string {
   return s.replace(/\\/g, '\\\\').replace(/%/g, '\\%').replace(/_/g, '\\_');
 }
+
+/**
+ * Conservative per-char-class embedding-token weights (markdown chunker v4).
+ *
+ * Why this exists: the chunker's "word" counting drastically UNDER-counts
+ * whitespace-less ASCII runs (a 150-char URL = 1 whitespace word), so
+ * word-based size targets can emit chunks that overflow an embedding
+ * server's per-request token limit. Measured on a local Qwen3-embedding
+ * llama-server stack:
+ *   - URL/phone/email-dense text tokenizes at ~1.6 chars/token
+ *   - base64-ish / minified blobs approach ~1.3 chars/token (worst case)
+ *   - Korean prose tokenizes NO WORSE than 1 char/token in practice
+ *
+ * Weights are deliberately HIGH (tokens are overestimated) so any cap
+ * based on this estimate is safe against real tokenizers:
+ *   - CJK char        → 1.0 token  (real CJK prose is cheaper)
+ *   - other non-space → 0.75 token (≈1.33 chars/token, covers base64)
+ *   - whitespace      → 0.1 token  (mostly folds into neighbor tokens)
+ */
+export const EMBED_TOKEN_WEIGHT_CJK = 1.0;
+export const EMBED_TOKEN_WEIGHT_OTHER = 0.75;
+export const EMBED_TOKEN_WEIGHT_WS = 0.1;
+
+/** BMP CJK check by UTF-16 code unit — same ranges as CJK_SLUG_CHARS. */
+export function isCJKCodeUnit(code: number): boolean {
+  return (
+    (code >= 0x4e00 && code <= 0x9fff) || // Han
+    (code >= 0x3040 && code <= 0x309f) || // Hiragana
+    (code >= 0x30a0 && code <= 0x30ff) || // Katakana
+    (code >= 0xac00 && code <= 0xd7af)    // Hangul Syllables
+  );
+}
+
+/**
+ * Per-code-unit token weight. Unrecognized whitespace (exotic Unicode
+ * spaces) intentionally falls into OTHER — that only overestimates.
+ */
+export function charEmbedTokenWeight(code: number): number {
+  if (isCJKCodeUnit(code)) return EMBED_TOKEN_WEIGHT_CJK;
+  if (
+    code === 0x20 || (code >= 0x09 && code <= 0x0d) ||
+    code === 0xa0 || code === 0x3000
+  ) {
+    return EMBED_TOKEN_WEIGHT_WS;
+  }
+  return EMBED_TOKEN_WEIGHT_OTHER;
+}
+
+/**
+ * Tokenizer-free embedding-token estimate (conservative overestimate).
+ * See weight docs above. Astral chars count as 2 OTHER code units —
+ * another overestimate, which is the safe direction.
+ */
+export function estimateEmbeddingTokens(s: string): number {
+  if (s.length === 0) return 0;
+  let est = 0;
+  for (let i = 0; i < s.length; i++) {
+    est += charEmbedTokenWeight(s.charCodeAt(i));
+  }
+  return Math.ceil(est);
+}

src/core/operations.ts

@@ -769,7 +769,7 @@ const get_page: Operation = {
 
 const put_page: Operation = {
   name: 'put_page',
-  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. On the CLI, `gbrain put SLUG --file PATH` reads content from a file (also `--content` or stdin). For provenance write-through and a binary-NUL guard, prefer `gbrain capture --file PATH --slug SLUG` (v0.39.3.0).',
+  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. For large content on Windows (pipe-buffer limit ~45KB) or any file-as-input workflow, use `gbrain capture --file PATH --slug SLUG` — capture reads the file as a Buffer with a binary-NUL guard and adds provenance write-through (v0.39.3.0).',
   params: {
     slug: { type: 'string', required: true, description: 'Page slug' },
     content: { type: 'string', required: true, description: 'Full markdown content with YAML frontmatter' },
@@ -1384,10 +1384,7 @@ const list_pages: Operation = {
   params: {
     type: { type: 'string', description: 'Filter by page type' },
     tag: { type: 'string', description: 'Filter by tag' },
-    limit: { type: 'number', description: 'Max results (default 50, capped at 100 — use offset to paginate beyond)' },
-    // #2876: the 100-row cap was silent and there was no way past it even
-    // though both engines already support OFFSET on listPages.
-    offset: { type: 'number', description: 'Skip first N results (pagination; pair with limit)' },
+    limit: { type: 'number', description: 'Max results (default 50)' },
     // v0.29 — surface filter that already exists on PageFilters.
     updated_after: {
       type: 'string',
@@ -1418,10 +1415,6 @@ const list_pages: Operation = {
       type: p.type as any,
       tag: p.tag as string,
       limit: clampSearchLimit(p.limit as number | undefined, 50, 100),
-      // #2876: thread pagination through (engines already honor offset).
-      offset: Number.isFinite(p.offset as number) && (p.offset as number) > 0
-        ? Math.floor(p.offset as number)
-        : undefined,
       includeDeleted: (p.include_deleted as boolean) === true,
       updated_after: typeof p.updated_after === 'string' ? p.updated_after : undefined,
       sort,

test/chunker-version-gate.test.ts

@@ -15,19 +15,22 @@ import { describe, test, expect } from 'bun:test';
 import { CHUNKER_VERSION } from '../src/core/chunkers/code.ts';
 
 describe('Layer 12 — CHUNKER_VERSION constant', () => {
-  test('bumped to 4 for Cathedral II', () => {
+  test('bumped to 5 for the estimated-token hard cap', () => {
     // v3: v0.19.0 Chonkie parity (tokenizer + small-sibling merge).
     // v4: v0.20.0 Cathedral II (qualified names + parent scope + doc_comment
     //     + fence extraction + chunk-grain FTS). Folded into content_hash
     //     so any bump forces clean re-chunks on next sync.
-    expect(CHUNKER_VERSION).toBe(4);
+    // v5: estimated-token hard cap on AST-path chunks (capCodeChunks) so
+    //     un-subdividable giant nodes can't overflow strict embedding
+    //     server token limits.
+    expect(CHUNKER_VERSION).toBe(5);
   });
 
   test('is stable across imports (not recomputed at call time)', async () => {
     const a = (await import('../src/core/chunkers/code.ts')).CHUNKER_VERSION;
     const b = (await import('../src/core/chunkers/code.ts')).CHUNKER_VERSION;
     expect(a).toBe(b);
-    expect(a).toBe(4);
+    expect(a).toBe(5);
   });
 });
 

test/chunkers/code.test.ts

@@ -10,8 +10,8 @@ import { describe, test, expect } from 'bun:test';
 import { chunkCodeText, detectCodeLanguage, CHUNKER_VERSION } from '../../src/core/chunkers/code.ts';
 
 describe('CHUNKER_VERSION', () => {
-  test('v0.20.0 Cathedral II Layer 12 bumped to 4', () => {
-    expect(CHUNKER_VERSION).toBe(4);
+  test('v5: estimated-token hard cap on AST-path chunks', () => {
+    expect(CHUNKER_VERSION).toBe(5);
   });
 });
 

test/chunkers/recursive.test.ts

@@ -135,13 +135,14 @@ describe('Recursive Text Chunker', () => {
 });
 
 describe('CJK chunking (v0.32.7)', () => {
-  test('MARKDOWN_CHUNKER_VERSION is 3', async () => {
+  test('MARKDOWN_CHUNKER_VERSION is 4', async () => {
     // v0.40.3.0: bumped 2→3 to signal the post-upgrade reembed sweep that
-    // contextual retrieval wrapping is now applied at embed time. Chunk
-    // boundaries themselves are unchanged; the bump forces re-embed for
-    // pages where chunker_version < 3.
+    // contextual retrieval wrapping is now applied at embed time.
+    // v4: estimated-token hard cap + whitespace-word undercount floor
+    // (URL-dense docs produced chunks past strict embedding server token
+    // limits). Boundary change → forces re-chunk for chunker_version < 4.
     const mod = await import('../../src/core/chunkers/recursive.ts');
-    expect(mod.MARKDOWN_CHUNKER_VERSION).toBe(3);
+    expect(mod.MARKDOWN_CHUNKER_VERSION).toBe(4);
   });
 
   test('long pure-Chinese paragraph splits into multiple chunks', () => {

test/chunkers/token-cap.test.ts

@@ -0,0 +1,195 @@
+/**
+ * Markdown chunker v4 / code chunker v5 — estimated-token hard cap
+ * regression tests.
+ *
+ * Reproduces a field failure: a local llama-server embedding backend
+ * (`-ub 2048`) crashes deterministically (trace/BPT trap → EOF at the
+ * client) when a single chunk exceeds ~2,050 real tokens. Two content
+ * shapes triggered it:
+ *
+ *   1. Korean docs carrying one long source URL per line.
+ *      The URLs' ASCII mass pushes CJK density below 0.30, flipping
+ *      countCJKAwareWords to whitespace counting, where a 150-char URL
+ *      counts as ONE word → chunks ballooned to 3-4K chars ≈ 2,000+
+ *      real tokens (URL soup tokenizes at ~1.6 chars/token).
+ *
+ *   2. Large JSON code blocks (~7K chars) that the word pipeline
+ *      undercounts the same way (few whitespace tokens).
+ *
+ * The fix: every emitted chunk must satisfy
+ *   estimateEmbeddingTokens(chunk) <= maxTokens (default 1500)
+ * where the estimate deliberately OVERSTATES real tokenizer counts.
+ */
+
+import { describe, test, expect } from 'bun:test';
+import { chunkText, capByEstimatedTokens, DEFAULT_MAX_EST_TOKENS } from '../../src/core/chunkers/recursive.ts';
+import { chunkCodeText } from '../../src/core/chunkers/code.ts';
+import { estimateEmbeddingTokens } from '../../src/core/cjk.ts';
+
+/** Synthesize the failing shape: Korean rollup lines each ending in a long Notion URL. */
+function urlDenseKoreanRollup(lines: number): string {
+  const out: string[] = ['# 링크가 줄마다 붙는 한국어 예시 문서', ''];
+  for (let i = 0; i < lines; i++) {
+    const hex32 = (i * 2654435761 >>> 0).toString(16).padStart(8, '0').repeat(4);
+    out.push(
+      `- **항목 ${i}**: 이 줄은 청커 동작 검증을 위한 의미 없는 한국어 예시 문장입니다 · 전화 000-0000-${String(1000 + i)} · ` +
+      `이메일 user${i}@example.com · 링크: https://docs.example.com/pages/${hex32}?v=abcdef0123456789&ref=sample`,
+    );
+  }
+  return out.join('\n');
+}
+
+/** Synthesize a large pretty-printed JSON block with CJK values. */
+function bigJsonBlock(targetChars: number): string {
+  const entries: string[] = [];
+  let i = 0;
+  let len = 0;
+  while (len < targetChars) {
+    const row =
+      `  "item_${i}": { "name": "예시-${i}", "url": "https://example.com/api/v2/items/${i}?token=abc${i}def", "qty": ${i % 100}, "memo": "한국어 값이 섞인 예시 데이터" }`;
+    entries.push(row);
+    len += row.length;
+    i++;
+  }
+  return `{\n${entries.join(',\n')}\n}`;
+}
+
+describe('v4 estimated-token cap — URL-dense Korean doc (field-failure shape)', () => {
+  test('every chunk stays under the estimated-token cap', () => {
+    const md = urlDenseKoreanRollup(60);
+    const chunks = chunkText(md);
+    expect(chunks.length).toBeGreaterThan(0);
+    for (const c of chunks) {
+      expect(estimateEmbeddingTokens(c.text)).toBeLessThanOrEqual(DEFAULT_MAX_EST_TOKENS);
+    }
+  });
+
+  test('no chunk reaches the measured 3K-char danger zone for URL soup', () => {
+    const md = urlDenseKoreanRollup(60);
+    const chunks = chunkText(md);
+    // 1500 est tokens at the OTHER weight (0.75/char) bounds chunks to
+    // ~2,000 chars for pure ASCII — well under the ~3,300 chars where
+    // URL-dense content crosses ~2,050 real tokens (1.6 chars/token).
+    for (const c of chunks) {
+      expect(c.text.length).toBeLessThanOrEqual(2600);
+    }
+  });
+
+  test('content is preserved (no lines dropped by the cap)', () => {
+    const md = urlDenseKoreanRollup(60);
+    const chunks = chunkText(md);
+    const joined = chunks.map((c) => c.text).join('\n');
+    // Spot-check first / middle / last rollup lines survive chunking.
+    for (const marker of ['항목 0', '항목 30', '항목 59']) {
+      expect(joined).toContain(marker);
+    }
+  });
+});
+
+describe('v4 estimated-token cap — large JSON blocks', () => {
+  test('7K-char pretty JSON through the prose path stays under the cap', () => {
+    const md = `설정 파일 원문 보존:\n\n\`\`\`\n${bigJsonBlock(7000)}\n\`\`\`\n`;
+    const chunks = chunkText(md);
+    expect(chunks.length).toBeGreaterThan(1);
+    for (const c of chunks) {
+      expect(estimateEmbeddingTokens(c.text)).toBeLessThanOrEqual(DEFAULT_MAX_EST_TOKENS);
+    }
+  });
+
+  test('7K-char minified JSON (single whitespace-less token) stays under the cap', () => {
+    const minified = bigJsonBlock(7000).replace(/\n\s*/g, '');
+    const chunks = chunkText(minified);
+    expect(chunks.length).toBeGreaterThan(1);
+    for (const c of chunks) {
+      expect(estimateEmbeddingTokens(c.text)).toBeLessThanOrEqual(DEFAULT_MAX_EST_TOKENS);
+    }
+  });
+
+  test('json fence via the code chunker stays under the cap (+header slack)', async () => {
+    const chunks = await chunkCodeText(bigJsonBlock(7000), 'fence.json');
+    expect(chunks.length).toBeGreaterThan(0);
+    for (const c of chunks) {
+      // buildChunk prepends a short "[JSON] fence.json:…" header AFTER the
+      // body-level cap; allow ~60 est tokens of header slack. Real-token
+      // safety margin (2,050 − overestimated 1,500) absorbs this easily.
+      expect(estimateEmbeddingTokens(c.text)).toBeLessThanOrEqual(DEFAULT_MAX_EST_TOKENS + 60);
+    }
+  });
+});
+
+describe('v4 word-count floor — behavior preserved for normal content', () => {
+  test('Latin prose chunking is unchanged by the floor (avg word < 6 chars)', () => {
+    const prose = Array.from({ length: 120 }, (_, i) =>
+      `This is sentence number ${i} and it talks about ordinary things in plain words.`,
+    ).join(' ');
+    const chunks = chunkText(prose);
+    // Historical behavior: ~1,560 whitespace words → multiple ~300-word chunks.
+    expect(chunks.length).toBeGreaterThan(3);
+    for (const c of chunks) {
+      const words = c.text.split(/\s+/).length;
+      expect(words).toBeLessThanOrEqual(300 * 1.5 + 50); // merge cap + overlap
+    }
+  });
+
+  test('Korean prose (CJK-dense, no URLs) never triggers the token cap', () => {
+    const prose = Array.from({ length: 80 }, (_, i) =>
+      `이 문장은 순수 한국어 산문의 청킹 동작을 확인하기 위한 ${i}번째 예시 문장입니다.`,
+    ).join(' ');
+    const chunks = chunkText(prose);
+    expect(chunks.length).toBeGreaterThan(1);
+    for (const c of chunks) {
+      // CJK-dense chunks are char-counted (≈450 max) — nowhere near 1500.
+      expect(estimateEmbeddingTokens(c.text)).toBeLessThanOrEqual(700);
+    }
+  });
+});
+
+describe('capByEstimatedTokens unit behavior', () => {
+  test('returns input unchanged when under the cap', () => {
+    expect(capByEstimatedTokens('short text', 1500)).toEqual(['short text']);
+    expect(capByEstimatedTokens('', 1500)).toEqual([]);
+  });
+
+  test('prefers newline cut points within the lookback window', () => {
+    const line = 'x'.repeat(100);
+    const text = Array.from({ length: 40 }, () => line).join('\n');
+    const pieces = capByEstimatedTokens(text, 1000);
+    expect(pieces.length).toBeGreaterThan(1);
+    for (const p of pieces) {
+      // Every piece should be whole lines (multiples of the 100-char line).
+      for (const l of p.split('\n')) {
+        expect(l).toBe(line);
+      }
+    }
+  });
+
+  test('makes forward progress on whitespace-less input (hard cut)', () => {
+    const blob = 'a'.repeat(10_000);
+    const pieces = capByEstimatedTokens(blob, 1000);
+    expect(pieces.length).toBeGreaterThan(1);
+    expect(pieces.join('')).toBe(blob);
+    for (const p of pieces) {
+      expect(estimateEmbeddingTokens(p)).toBeLessThanOrEqual(1000);
+    }
+  });
+});
+
+describe('estimateEmbeddingTokens — weight sanity', () => {
+  test('overestimates URL-dense ASCII (0.75/char ≥ measured ~0.63/char)', () => {
+    const url = 'https://docs.example.com/pages/a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4?v=abc&ref=sample';
+    const est = estimateEmbeddingTokens(url);
+    expect(est).toBeGreaterThanOrEqual(Math.floor(url.length * 0.7));
+  });
+
+  test('counts CJK at 1 token/char', () => {
+    expect(estimateEmbeddingTokens('가나다라마')).toBe(5);
+  });
+
+  test('whitespace is nearly free', () => {
+    expect(estimateEmbeddingTokens('   \n\t  ')).toBeLessThanOrEqual(1);
+  });
+
+  test('empty string is 0', () => {
+    expect(estimateEmbeddingTokens('')).toBe(0);
+  });
+});

test/cli-args.test.ts

@@ -1,41 +1,8 @@
 import { describe, expect, test } from 'bun:test';
-import { mkdtempSync, rmSync, writeFileSync } from 'fs';
-import { tmpdir } from 'os';
-import { join } from 'path';
 import { parseOpArgs } from '../src/cli.ts';
 import { operationsByName } from '../src/core/operations.ts';
 
 describe('parseOpArgs', () => {
-  // #380: `gbrain put SLUG --file PATH` reads content from the file instead
-  // of silently swallowing the flag and creating an empty page.
-  test('put --file reads the stdin param (content) from a file', () => {
-    const dir = mkdtempSync(join(tmpdir(), 'gbrain-put-file-'));
-    try {
-      const pagePath = join(dir, 'page.md');
-      writeFileSync(pagePath, '# From file\n\nBody loaded from --file.\n');
-      const params = parseOpArgs(operationsByName.put_page, ['concepts/from-file', '--file', pagePath]);
-      expect(params.slug).toBe('concepts/from-file');
-      expect(params.content).toBe('# From file\n\nBody loaded from --file.\n');
-    } finally {
-      rmSync(dir, { recursive: true, force: true });
-    }
-  });
-
-  // #380 regression guard: undeclared-but-honored flags must keep passing
-  // through when unknown flags become hard errors (--source is read by
-  // makeContext; --json by the output seam; --dry-run by ctx.dryRun).
-  test('pass-through allowlist flags survive on ops that do not declare them', () => {
-    const params = parseOpArgs(operationsByName.get_page, [
-      'people/alice-example', '--source', 'wiki', '--json', '--dry-run',
-    ]);
-    expect(params).toEqual({
-      slug: 'people/alice-example',
-      source: 'wiki',
-      json: true,
-      dry_run: true,
-    });
-  });
-
   test('--no-<boolean> maps to false without consuming the next flag', () => {
     const params = parseOpArgs(operationsByName.query, [
       'freshEmbedSourceScope code source',

test/cli.test.ts

@@ -1,5 +1,5 @@
 import { describe, test, expect } from 'bun:test';
-import { existsSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'fs';
+import { existsSync, mkdtempSync, readFileSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 
@@ -120,76 +120,6 @@ describe('CLI dispatch integration', () => {
     expect(exitCode).toBe(0);
   });
 
-  // #380 / PR #856: put --help documents the --file input path.
-  test('put --help documents --file input', async () => {
-    const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'put', '--help'], {
-      cwd: repoRoot,
-      stdout: 'pipe',
-      stderr: 'pipe',
-    });
-    const stdout = await new Response(proc.stdout).text();
-    const exitCode = await proc.exited;
-    expect(stdout).toContain('Usage: gbrain put');
-    expect(stdout).toContain('--file <path>');
-    expect(exitCode).toBe(0);
-  });
-
-  // #380: unknown flags on shared ops are a hard error (previously silently
-  // swallowed into params — `put --file` created empty pages). parseOpArgs
-  // runs BEFORE engine connect, so the error must fire without a brain.
-  test('unknown shared-op flags fail before DB connection', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-unknown-flag-'));
-    try {
-      const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'get', 'people/alice', '--bogus'], {
-        cwd: repoRoot,
-        stdout: 'pipe',
-        stderr: 'pipe',
-        env: isolatedEnv(home),
-      });
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('Unknown option for gbrain get: --bogus');
-      expect(stderr).not.toContain('No brain configured');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
-  test('put rejects combining --file and --content', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-conflict-'));
-    try {
-      const pagePath = join(home, 'page.md');
-      writeFileSync(pagePath, 'file body\n');
-      const proc = Bun.spawn(
-        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--content', 'inline', '--file', pagePath],
-        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
-      );
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('use only one of --file, --content, or stdin');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
-  test('put --file with a missing path errors instead of writing an empty page', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-missing-file-'));
-    try {
-      const proc = Bun.spawn(
-        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--file', join(home, 'nope.md')],
-        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
-      );
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('cannot read --file');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
   test('upgrade --help prints usage without running upgrade', async () => {
     const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'upgrade', '--help'], {
       cwd: repoRoot,

test/list-pages-offset.test.ts

@@ -1,55 +0,0 @@
-import { describe, test, expect } from 'bun:test';
-import { operationsByName } from '../src/core/operations.ts';
-
-/**
- * #2876: `gbrain list --limit` silently clamped at 100 with no pagination.
- * list_pages now declares `offset` (both engines already supported it on
- * PageFilters) and the limit description discloses the 100-row cap.
- */
-describe('list_pages pagination (#2876)', () => {
-  const listPagesOp = operationsByName.list_pages;
-
-  function makeCtx(captured: unknown[]) {
-    return {
-      engine: {
-        listPages: async (filters: unknown) => {
-          captured.push(filters);
-          return [];
-        },
-      },
-      config: { engine: 'pglite' },
-      logger: { info() {}, warn() {}, error() {} },
-      dryRun: false,
-      remote: false,
-      sourceId: 'default',
-    } as any;
-  }
-
-  test('declares offset param and discloses the 100-row cap on limit', () => {
-    expect(listPagesOp.params.offset).toBeDefined();
-    expect(listPagesOp.params.offset.type).toBe('number');
-    expect(listPagesOp.params.limit.description).toContain('100');
-  });
-
-  test('threads offset through to engine.listPages', async () => {
-    const captured: any[] = [];
-    await listPagesOp.handler(makeCtx(captured), { limit: 10, offset: 30 });
-    expect(captured[0].offset).toBe(30);
-    expect(captured[0].limit).toBe(10);
-  });
-
-  test('drops negative, non-finite, and zero offsets', async () => {
-    const captured: any[] = [];
-    const ctx = makeCtx(captured);
-    await listPagesOp.handler(ctx, { offset: -5 });
-    await listPagesOp.handler(ctx, { offset: Infinity });
-    await listPagesOp.handler(ctx, { offset: 0 });
-    for (const f of captured) expect(f.offset).toBeUndefined();
-  });
-
-  test('floors fractional offsets', async () => {
-    const captured: any[] = [];
-    await listPagesOp.handler(makeCtx(captured), { offset: 7.9 });
-    expect(captured[0].offset).toBe(7);
-  });
-});