ollama-intern-mcp 2.0.0 → 2.0.1

package/README.md

@@ -17,7 +17,7 @@
 
 An MCP server that gives Claude Code a **local intern** with rules, tiers, a desk, and a filing cabinet. Claude picks the _tool_; the tool picks the _tier_ (Instant / Workhorse / Deep / Embed); the tier writes a file you can open next week.
 
-**Also drives [Hermes Agent](https://github.com/NousResearch/Hermes) on `hermes3:8b`** — validated end-to-end 2026-04-19. The default ladder is `hermes3:8b`; `qwen3:*` is the alternate rail. See [Use with Hermes](#use-with-hermes) below.
+**Also drives [Hermes Agent](https://github.com/NousResearch/hermes-agent) on `hermes3:8b`** — validated end-to-end 2026-04-19. The default ladder is `hermes3:8b`; `qwen3:*` is the alternate rail. See [Use with Hermes](#use-with-hermes) below.
 
 No cloud. No telemetry. No "autonomous" anything. Every call shows its work.
 
@@ -87,13 +87,11 @@ The full tool reference lives in the [handbook](https://mcp-tool-shop-org.github
 
 ## Install
 
-```bash
-npm install -g ollama-intern-mcp
-```
+Requires [Ollama](https://ollama.com) running locally and the tier models pulled (see [Model pulls](#model-pulls) below).
 
-Requires [Ollama](https://ollama.com) running locally and the tier models pulled.
+### Claude Code (recommended)
 
-### Claude Code
+Most users install this by adding it to their Claude Code MCP server config — no global install required. Claude Code runs the server on demand via `npx`:
 
 ```json
 {
@@ -114,9 +112,17 @@ Requires [Ollama](https://ollama.com) running locally and the tier models pulled
 
 Same block, written to `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS) or `%APPDATA%\Claude\claude_desktop_config.json` (Windows).
 
+### Global install (advanced)
+
+Only needed if you want the binary on your `PATH` for ad-hoc use outside Claude Code:
+
+```bash
+npm install -g ollama-intern-mcp
+```
+
 ### Use with Hermes
 
-This MCP was validated end-to-end with [Hermes Agent](https://github.com/NousResearch/Hermes) against `hermes3:8b` on Ollama (2026-04-19). Hermes is an external agent that *calls into* this MCP's frozen primitive surface — it does the planning, we do the work.
+This MCP was validated end-to-end with [Hermes Agent](https://github.com/NousResearch/hermes-agent) against `hermes3:8b` on Ollama (2026-04-19). Hermes is an external agent that *calls into* this MCP's frozen primitive surface — it does the planning, we do the work.
 
 Reference config ([hermes.config.example.yaml](hermes.config.example.yaml) in this repo):
 
@@ -273,7 +279,7 @@ Built to the [Shipcheck](https://github.com/mcp-tool-shop-org/shipcheck) bar. Ha
 - **A. Security** — SECURITY.md, threat model, no telemetry, path-safety, `confirm_write` on protected paths
 - **B. Errors** — structured shape across all tool results; no raw stacks
 - **C. Docs** — README current, CHANGELOG, LICENSE; tool schemas self-document
-- **D. Hygiene** — `npm run verify` (395 tests), CI with dep scanning, Dependabot, lockfile, `engines.node`
+- **D. Hygiene** — `npm run verify` (481 tests), CI with dep scanning, Dependabot, lockfile, `engines.node`
 
 ---
 
@@ -282,7 +288,7 @@ Built to the [Shipcheck](https://github.com/mcp-tool-shop-org/shipcheck) bar. Ha
 - **Phase 1 — Delegation Spine** ✓ shipped: atom surface, uniform envelope, tiered routing, guardrails
 - **Phase 2 — Truth Spine** ✓ shipped: schema v2 chunking, BM25 + RRF, living corpora, evidence-backed briefs, retrieval eval pack
 - **Phase 3 — Pack & Artifact Spine** ✓ shipped: fixed-pipeline packs with durable artifacts + continuity tier
-- **Phase 4 — Adoption Spine** — real-use observation on the RTX 5080, hardening the rough edges that surface
+- **Phase 4 — Adoption Spine** ✓ v2.0.1: three-stage health pass hardened corpus (TOCTOU, 50 MB file cap, symlink rejection, atomic writes, per-file failure capture), tool path traversal, observability (semaphore wait events, timeout error context, profile env-override logging, prewarm cold-start signal), test safety (module-load env snapshot across 10 files, `tools/call` E2E). Troubleshooting handbook + hardware minimums added for operators.
 - **Phase 5 — M5 Max benchmarks** — publishable numbers once the hardware lands (~2026-04-24)
 
 Phase by hardening layer. The atom/pack/artifact surface stays frozen.

package/SECURITY.md

@@ -13,9 +13,11 @@ The primary risks are not network-facing. They are:
 
 ## Reporting
 
-Email: 64996768+mcp-tool-shop@users.noreply.github.com
+Please do **not** file public issues for security bugs.
 
-Please do not file public issues for security bugs. We will acknowledge within 72 hours.
+Open a private [security advisory](https://github.com/mcp-tool-shop-org/ollama-intern-mcp/security/advisories/new) via the **Security** tab on this repo. The advisory stays private until a fix is ready. We will acknowledge within 72 hours.
+
+The repo is owned by **mcp-tool-shop-org**; advisories route to the org maintainers.
 
 ## Supported Versions
 

package/dist/corpus/indexer.d.ts

@@ -17,6 +17,21 @@ export interface IndexParams {
     chunk_chars?: number;
     chunk_overlap?: number;
     client: OllamaClient;
+    /**
+     * Optional progress callback invoked after each input file is processed
+     * (success OR failure). `done` counts files that have been handled,
+     * `total` is params.paths.length, `currentPath` is the path just
+     * processed. Safe to ignore — purely observability. A second callback
+     * fires after each embed batch with done=total+batchIdx, so callers can
+     * see embed progress too; MCP tool layer can filter on `currentPath`
+     * starting with "embed:" to distinguish.
+     */
+    onProgress?: (done: number, total: number, currentPath: string) => void;
+}
+/** One entry per path that could not be read/hashed during indexing. */
+export interface IndexFailedPath {
+    path: string;
+    reason: string;
 }
 export interface IndexReport {
     name: string;
@@ -35,6 +50,13 @@ export interface IndexReport {
      * silent :latest drift.
      */
     embed_model_resolved: string | null;
+    /**
+     * Paths that could not be read (size cap, symlink, permission denied,
+     * TOCTOU, etc.) during this index run. Indexing continues past these so
+     * one bad file in a batch of 1000 no longer halts the whole pass. Empty
+     * array on the happy path.
+     */
+    failed_paths: IndexFailedPath[];
 }
 export declare function indexCorpus(params: IndexParams): Promise<IndexReport>;
 //# sourceMappingURL=indexer.d.ts.map

package/dist/corpus/indexer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"indexer.d.ts","sourceRoot":"","sources":["../../src/corpus/indexer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAQjD,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,EAAE,YAAY,CAAC;CACtB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,EAAE,MAAM,CAAC;IACtB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;IACtB,qBAAqB,EAAE,MAAM,CAAC;IAC9B,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;IACnB;;;;;OAKG;IACH,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;CACrC;AASD,wBAAsB,WAAW,CAAC,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,WAAW,CAAC,CAgN3E"}
+{"version":3,"file":"indexer.d.ts","sourceRoot":"","sources":["../../src/corpus/indexer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAUjD,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,EAAE,YAAY,CAAC;IACrB;;;;;;;;OAQG;IACH,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC;CACzE;AAED,wEAAwE;AACxE,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,EAAE,MAAM,CAAC;IACtB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;IACtB,qBAAqB,EAAE,MAAM,CAAC;IAC9B,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;IACnB;;;;;OAKG;IACH,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC;;;;;OAKG;IACH,YAAY,EAAE,eAAe,EAAE,CAAC;CACjC;AAiDD,wBAAsB,WAAW,CAAC,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,WAAW,CAAC,CAoO3E"}

package/dist/corpus/indexer.js

@@ -9,7 +9,7 @@
  * This means `index` can be called repeatedly in daily use without
  * burning the embed tier on unchanged content.
  */
-import { readFile, stat } from "node:fs/promises";
+import { readFile, stat, realpath, lstat } from "node:fs/promises";
 import { resolve } from "node:path";
 import { createHash } from "node:crypto";
 import { chunkDocument, DEFAULT_CHUNK } from "./chunker.js";
@@ -17,11 +17,38 @@ import { CORPUS_SCHEMA_VERSION, loadCorpus, saveCorpus } from "./storage.js";
 import { MANIFEST_SCHEMA_VERSION, loadManifest, saveManifest } from "./manifest.js";
 import { InternError } from "../errors.js";
 const EMBED_BATCH = 64;
+/** Hard cap on input file size. Prevents OOM from a user pointing at a 100GB file. */
+const MAX_FILE_BYTES = 50 * 1024 * 1024;
+/**
+ * Read a file and hash it with TOCTOU protection.
+ *
+ * Invariant: a successful return means "the file was in exactly this state
+ * (size + mtime) when we hashed it". We stat BEFORE read (to enforce size
+ * cap and symlink rejection without reading bytes first), then stat AGAIN
+ * after read and fail if size or mtime drifted — that means the file
+ * mutated mid-read and the hash doesn't match the returned content.
+ */
 async function sha256File(path) {
-    const content = await readFile(path, "utf8");
+    // Symlink check FIRST — reject before any size/read work so a symlink to
+    // a sensitive file can't leak even partial bytes via error messages.
+    const lst = await lstat(path);
+    if (lst.isSymbolicLink()) {
+        throw new InternError("SOURCE_PATH_NOT_FOUND", `Refusing to index symlink: ${path}`, "Pass the real file path, not a symlink. Symlinks are rejected to avoid traversal into unintended targets.", false);
+    }
+    // Resolve to a real path as a belt-and-suspenders check against
+    // intermediate symlinked directories.
+    const realPath = await realpath(path);
+    const stBefore = await stat(realPath);
+    if (stBefore.size > MAX_FILE_BYTES) {
+        throw new InternError("SOURCE_PATH_NOT_FOUND", `File exceeds max size (${stBefore.size} bytes > ${MAX_FILE_BYTES} bytes cap): ${path}`, `Split the file or raise the cap. The 50MB limit exists to prevent OOM from a user pointing at a huge file.`, false);
+    }
+    const content = await readFile(realPath, "utf8");
     const hash = "sha256:" + createHash("sha256").update(content).digest("hex");
-    const st = await stat(path);
-    return { hash, mtime: st.mtime.toISOString(), content };
+    const stAfter = await stat(realPath);
+    if (stAfter.size !== stBefore.size || stAfter.mtimeMs !== stBefore.mtimeMs) {
+        throw new InternError("SOURCE_PATH_NOT_FOUND", `File mutated during read (TOCTOU): ${path}`, "Another process wrote to the file while we were hashing it. Re-run the index.", true);
+    }
+    return { hash, mtime: stBefore.mtime.toISOString(), content };
 }
 export async function indexCorpus(params) {
     const t0 = Date.now();
@@ -46,6 +73,11 @@ export async function indexCorpus(params) {
             throw err;
         }
     }
+    // Refuse silent embed-model mismatch. Mixing vectors from different
+    // embed models in one corpus ruins search — the space isn't shared.
+    if (existing && existing.model_version !== params.model) {
+        throw new InternError("SCHEMA_INVALID", `Corpus "${params.name}" was indexed with embed model "${existing.model_version}"; refusing to re-index with "${params.model}".`, `Re-index with the original model, or pass a different corpus name to keep the new model isolated.`, false);
+    }
     const reusable = new Map();
     if (existing && existing.model_version === params.model) {
         for (const c of existing.chunks) {
@@ -70,6 +102,7 @@ export async function indexCorpus(params) {
     // Pass 1: read + hash every input, reuse where possible, collect chunks to embed.
     const toEmbedTexts = [];
     const toEmbedMeta = [];
+    const failedPaths = [];
     for (const rawPath of params.paths) {
         const absPath = resolve(rawPath);
         seenPaths.add(absPath);
@@ -78,7 +111,14 @@ export async function indexCorpus(params) {
             fileInfo = await sha256File(absPath);
         }
         catch (err) {
-            throw new InternError("SOURCE_PATH_NOT_FOUND", `Cannot read input file: ${rawPath} — ${err.message}`, "Check the path exists and is readable.", false);
+            // Stage C humanization: capture per-file failure and continue so one
+            // bad file in a batch of 1000 does not halt the whole pass. Caller
+            // sees failed_paths in the report.
+            failedPaths.push({
+                path: rawPath,
+                reason: err.message ?? String(err),
+            });
+            continue;
         }
         totalChars += fileInfo.content.length;
         const reuseKey = `${absPath}::${fileInfo.hash}`;
@@ -123,8 +163,14 @@ export async function indexCorpus(params) {
             }
             for (let j = 0; j < batch.length; j++) {
                 const meta = toEmbedMeta[i + j];
+                // ID is stable per (content-hash, chunk_index): re-indexing the
+                // same content produces the same chunk IDs, and a content change
+                // flips the hash so IDs can't collide across runs. Width of 6
+                // hex on the index is still >16M per file, but it's now scoped
+                // to file+content not to global run order.
+                const hashShort = meta.file_hash.replace(/^sha256:/, "").slice(0, 8);
                 allChunks.push({
-                    id: `${params.name}-${allChunks.length.toString(16).padStart(6, "0")}`,
+                    id: `${params.name}-${hashShort}-${meta.chunk_index.toString(16).padStart(6, "0")}`,
                     path: meta.path,
                     file_hash: meta.file_hash,
                     file_mtime: meta.file_mtime,
@@ -208,6 +254,7 @@ export async function indexCorpus(params) {
         dropped_files: droppedFiles,
         elapsed_ms: Date.now() - t0,
         embed_model_resolved: embedModelResolved,
+        failed_paths: failedPaths,
     };
 }
 //# sourceMappingURL=indexer.js.map

package/dist/corpus/indexer.js.map

@@ -1 +1 @@
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package/dist/corpus/manifest.d.ts

@@ -13,6 +13,12 @@
 export declare const MANIFEST_SCHEMA_VERSION = 2;
 export interface CorpusManifest {
     schema_version: number;
+    /**
+     * Package version that wrote this manifest. Loader rejects when this is
+     * higher than the current build — prevents a newer build writing a
+     * manifest that an older build would silently downgrade.
+     */
+    schema_version_written_by?: string;
     name: string;
     /** Absolute paths the corpus is declared to contain. */
     paths: string[];

package/dist/corpus/manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/corpus/manifest.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AASH,eAAO,MAAM,uBAAuB,IAAI,CAAC;AAEzC,MAAM,WAAW,cAAc;IAC7B,cAAc,EAAE,MAAM,CAAC;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,wDAAwD;IACxD,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,iFAAiF;IACjF,WAAW,EAAE,MAAM,CAAC;IACpB;;;;;;;;OAQG;IACH,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;CACpB;AAMD,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAEjD;AAED,wBAAsB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC,CAsB/E;AAED,wBAAsB,YAAY,CAAC,QAAQ,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAK1E"}
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/corpus/manifest.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAUH,eAAO,MAAM,uBAAuB,IAAI,CAAC;AAoFzC,MAAM,WAAW,cAAc;IAC7B,cAAc,EAAE,MAAM,CAAC;IACvB;;;;OAIG;IACH,yBAAyB,CAAC,EAAE,MAAM,CAAC;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,wDAAwD;IACxD,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,iFAAiF;IACjF,WAAW,EAAE,MAAM,CAAC;IACpB;;;;;;;;OAQG;IACH,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;CACpB;AAMD,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAEjD;AAED,wBAAsB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC,CAsB/E;AAED,wBAAsB,YAAY,CAAC,QAAQ,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAK1E"}

package/dist/corpus/manifest.js

@@ -11,12 +11,81 @@
  * manifest as a side effect; ollama_corpus_refresh reads it.
  */
 import { readFile, writeFile, mkdir } from "node:fs/promises";
-import { existsSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
-import { join, dirname } from "node:path";
+import { join, dirname, isAbsolute, normalize, sep } from "node:path";
+import { fileURLToPath } from "node:url";
 import { InternError } from "../errors.js";
 import { assertValidCorpusName } from "./storage.js";
 export const MANIFEST_SCHEMA_VERSION = 2;
+/**
+ * Package version stamped on every manifest write. Loader refuses to read
+ * a manifest whose writer version is newer than this build, to prevent
+ * silent downgrade even when schema_version matches.
+ */
+const MANIFEST_WRITER_VERSION = (() => {
+    try {
+        const pkgUrl = new URL("../../package.json", import.meta.url);
+        const raw = readFileSync(fileURLToPath(pkgUrl), "utf8");
+        return JSON.parse(raw).version ?? "0.0.0";
+    }
+    catch {
+        return "0.0.0";
+    }
+})();
+function compareVersions(a, b) {
+    const pa = a.split(".").map((n) => parseInt(n, 10));
+    const pb = b.split(".").map((n) => parseInt(n, 10));
+    for (let i = 0; i < 3; i++) {
+        const ai = pa[i] ?? 0;
+        const bi = pb[i] ?? 0;
+        if (Number.isNaN(ai) || Number.isNaN(bi))
+            return 0;
+        if (ai < bi)
+            return -1;
+        if (ai > bi)
+            return 1;
+    }
+    return 0;
+}
+/**
+ * Allowlisted roots a manifest's paths may live under. Defaults to the
+ * user's home dir; extendable via INTERN_CORPUS_ALLOWED_ROOTS (colon-
+ * separated on POSIX, semicolon-separated on Windows). A malicious
+ * manifest that points at /etc/shadow or C:/Windows/... is rejected here.
+ */
+function allowedRoots() {
+    const extra = process.env.INTERN_CORPUS_ALLOWED_ROOTS;
+    const roots = [homedir()];
+    if (extra) {
+        const sep = process.platform === "win32" ? ";" : ":";
+        for (const r of extra.split(sep)) {
+            if (r.trim())
+                roots.push(r.trim());
+        }
+    }
+    return roots.map((r) => normalize(r));
+}
+function assertSafePath(p) {
+    if (!isAbsolute(p)) {
+        throw new InternError("SCHEMA_INVALID", `Manifest path is not absolute: ${p}`, "All manifest paths must be absolute. Re-run ollama_corpus_index to rewrite the manifest with resolved paths.", false);
+    }
+    const normalized = normalize(p);
+    // Reject any `..` segments that survived normalize (shouldn't happen on
+    // absolute paths, but be defensive).
+    const segments = normalized.split(sep);
+    if (segments.includes("..")) {
+        throw new InternError("SCHEMA_INVALID", `Manifest path contains traversal segment after normalize: ${p}`, "Reject corpora whose manifest was hand-edited with `..` segments. Re-index with trusted paths.", false);
+    }
+    const roots = allowedRoots();
+    const ok = roots.some((root) => {
+        const r = root.endsWith(sep) ? root : root + sep;
+        return normalized === root || normalized.startsWith(r);
+    });
+    if (!ok) {
+        throw new InternError("SCHEMA_INVALID", `Manifest path is outside allowed roots: ${p}`, `Path must live under one of: ${roots.join(", ")}. Set INTERN_CORPUS_ALLOWED_ROOTS to add more.`, false);
+    }
+}
 function manifestDir() {
     return process.env.INTERN_CORPUS_DIR ?? join(homedir(), ".ollama-intern", "corpora");
 }

package/dist/corpus/manifest.js.map

@@ -1 +1 @@
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+{"version":3,"file":"manifest.js","sourceRoot":"","sources":["../../src/corpus/manifest.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAC9D,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,EAAE,MAAM,WAAW,CAAC;AACtE,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,cAAc,CAAC;AAErD,MAAM,CAAC,MAAM,uBAAuB,GAAG,CAAC,CAAC;AAEzC;;;;GAIG;AACH,MAAM,uBAAuB,GAAG,CAAC,GAAG,EAAE;IACpC,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,oBAAoB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC9D,MAAM,GAAG,GAAG,YAAY,CAAC,aAAa,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC,CAAC;QACxD,OAAQ,IAAI,CAAC,KAAK,CAAC,GAAG,CAA0B,CAAC,OAAO,IAAI,OAAO,CAAC;IACtE,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,OAAO,CAAC;IACjB,CAAC;AACH,CAAC,CAAC,EAAE,CAAC;AAEL,SAAS,eAAe,CAAC,CAAS,EAAE,CAAS;IAC3C,MAAM,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IACpD,MAAM,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IACpD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QACtB,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QACtB,IAAI,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC;YAAE,OAAO,CAAC,CAAC;QACnD,IAAI,EAAE,GAAG,EAAE;YAAE,OAAO,CAAC,CAAC,CAAC;QACvB,IAAI,EAAE,GAAG,EAAE;YAAE,OAAO,CAAC,CAAC;IACxB,CAAC;IACD,OAAO,CAAC,CAAC;AACX,CAAC;AAED;;;;;GAKG;AACH,SAAS,YAAY;IACnB,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,2BAA2B,CAAC;IACtD,MAAM,KAAK,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC;IAC1B,IAAI,KAAK,EAAE,CAAC;QACV,MAAM,GAAG,GAAG,OAAO,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QACrD,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACjC,IAAI,CAAC,CAAC,IAAI,EAAE;gBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;QACrC,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC;AACxC,CAAC;AAED,SAAS,cAAc,CAAC,CAAS;IAC/B,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;QACnB,MAAM,IAAI,WAAW,CACnB,gBAAgB,EAChB,kCAAkC,CAAC,EAAE,EACrC,8GAA8G,EAC9G,KAAK,CACN,CAAC;IACJ,CAAC;IACD,MAAM,UAAU,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;IAChC,wEAAwE;IACxE,qCAAqC;IACrC,MAAM,QAAQ,GAAG,UAAU,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IACvC,IAAI,QAAQ,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QAC5B,MAAM,IAAI,WAAW,CACnB,gBAAgB,EAChB,6DAA6D,CAAC,EAAE,EAChE,gGAAgG,EAChG,KAAK,CACN,CAAC;IACJ,CAAC;IACD,MAAM,KAAK,GAAG,YAAY,EAAE,CAAC;IAC7B,MAAM,EAAE,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE;QAC7B,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,GAAG,GAAG,CAAC;QACjD,OAAO,UAAU,KAAK,IAAI,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;IACzD,CAAC,CAAC,CAAC;IACH,IAAI,CAAC,EAAE,EAAE,CAAC;QACR,MAAM,IAAI,WAAW,CACnB,gBAAgB,EAChB,2CAA2C,CAAC,EAAE,EAC9C,gCAAgC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,gDAAgD,EAChG,KAAK,CACN,CAAC;IACJ,CAAC;AACH,CAAC;AA+BD,SAAS,WAAW;IAClB,OAAO,OAAO,CAAC,GAAG,CAAC,iBAAiB,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,gBAAgB,EAAE,SAAS,CAAC,CAAC;AACvF,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,IAAY;IACvC,OAAO,IAAI,CAAC,WAAW,EAAE,EAAE,GAAG,IAAI,gBAAgB,CAAC,CAAC;AACtD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,IAAY;IAC7C,qBAAqB,CAAC,IAAI,CAAC,CAAC;IAC5B,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC;IAChC,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IACnC,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IACzC,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAA0D,CAAC;IACxF,MAAM,KAAK,GAAG,MAAM,CAAC,cAAc,CAAC;IACpC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAChB,kEAAkE;QAClE,qEAAqE;QACrE,yDAAyD;QACzD,OAAO,EAAE,GAAI,MAAyB,EAAE,cAAc,EAAE,uBAAuB,EAAE,oBAAoB,EAAE,IAAI,EAAE,CAAC;IAChH,CAAC;IACD,IAAI,KAAK,KAAK,uBAAuB,EAAE,CAAC;QACtC,MAAM,IAAI,WAAW,CACnB,gBAAgB,EAChB,wBAAwB,IAAI,mBAAmB,KAAK,IAAI,SAAS,yBAAyB,uBAAuB,WAAW,IAAI,EAAE,EAClI,uCAAuC,IAAI,sEAAsE,EACjH,KAAK,CACN,CAAC;IACJ,CAAC;IACD,OAAO,MAAwB,CAAC;AAClC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,QAAwB;IACzD,qBAAqB,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;IACrC,MAAM,IAAI,GAAG,YAAY,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;IACzC,MAAM,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAChD,MAAM,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC;AACnE,CAAC"}

package/dist/corpus/storage.d.ts

@@ -8,6 +8,13 @@
  * Claude — search handlers strip them before returning.
  */
 export declare const CORPUS_SCHEMA_VERSION = 2;
+/**
+ * Hard cap on in-memory chunk count per corpus. A single JSON file that
+ * holds 1M+ chunks will blow past Node's string-length ceiling and OOM on
+ * write. If you hit this, split the corpus.
+ */
+export declare const MAX_CHUNKS = 100000;
+export declare const SCHEMA_WRITER_VERSION: string;
 export type ChunkType = "heading" | "paragraph" | "code" | "list" | "frontmatter";
 export interface CorpusChunk {
     id: string;
@@ -24,6 +31,13 @@ export interface CorpusChunk {
 }
 export interface CorpusFile {
     schema_version: number;
+    /**
+     * Package version that wrote this file. Used to reject the case where a
+     * newer build wrote the corpus and an older build (still on the same
+     * schema number) loads it and silently downgrades. Optional for
+     * backward-compat with files written before this field existed.
+     */
+    schema_version_written_by?: string;
     name: string;
     model_version: string;
     model_digest: string | null;
@@ -53,4 +67,25 @@ export interface CorpusSummary {
     bytes_on_disk: number;
 }
 export declare function listCorpora(): Promise<CorpusSummary[]>;
+/**
+ * Fast stale-detection primitive.
+ *
+ * Compares each manifest-declared path's current stat.mtime against the
+ * mtime stored in the corpus's chunks. Returns as soon as any drift is
+ * found — does NOT re-read file contents or re-hash, so it's cheap enough
+ * for callers to poll before deciding whether to pay the full refresh
+ * cost.
+ *
+ * Reasons:
+ *   - "no_corpus"   — corpus JSON missing
+ *   - "no_manifest" — manifest JSON missing
+ *   - "path_missing:<path>"  — manifest declares a path that isn't on disk
+ *   - "path_added:<path>"    — manifest declares a path the corpus has never seen
+ *   - "path_removed:<path>"  — corpus has a path the manifest no longer lists
+ *   - "mtime_drift:<path>"   — file's mtime is later than the corpus record
+ */
+export declare function isCorpusStale(name: string): Promise<{
+    stale: boolean;
+    reason?: string;
+}>;
 //# sourceMappingURL=storage.d.ts.map

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

@@ -1 +1 @@
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package/dist/corpus/storage.js

@@ -7,12 +7,52 @@
  * Raw vectors are stored (this file is the database), but they never reach
  * Claude — search handlers strip them before returning.
  */
-import { readFile, writeFile, mkdir, readdir, stat } from "node:fs/promises";
-import { existsSync } from "node:fs";
+import { readFile, mkdir, readdir, stat, rename, open, unlink } from "node:fs/promises";
+import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { join, dirname } from "node:path";
+import { fileURLToPath } from "node:url";
 import { InternError } from "../errors.js";
+import { loadManifest } from "./manifest.js";
 export const CORPUS_SCHEMA_VERSION = 2;
+/**
+ * Hard cap on in-memory chunk count per corpus. A single JSON file that
+ * holds 1M+ chunks will blow past Node's string-length ceiling and OOM on
+ * write. If you hit this, split the corpus.
+ */
+export const MAX_CHUNKS = 100_000;
+/**
+ * Stamped into every write so a newer-schema file is never silently
+ * downgraded by an older build. Resolved at import time from the running
+ * package version.
+ */
+const PKG_VERSION = (() => {
+    try {
+        const pkgUrl = new URL("../../package.json", import.meta.url);
+        const raw = readFileSync(fileURLToPath(pkgUrl), "utf8");
+        return JSON.parse(raw).version ?? "0.0.0";
+    }
+    catch {
+        return "0.0.0";
+    }
+})();
+export const SCHEMA_WRITER_VERSION = PKG_VERSION;
+/** semver-ish compare: returns -1 if a<b, 0 if equal, 1 if a>b. Falls back to 0 on parse error. */
+function compareVersions(a, b) {
+    const pa = a.split(".").map((n) => parseInt(n, 10));
+    const pb = b.split(".").map((n) => parseInt(n, 10));
+    for (let i = 0; i < 3; i++) {
+        const ai = pa[i] ?? 0;
+        const bi = pb[i] ?? 0;
+        if (Number.isNaN(ai) || Number.isNaN(bi))
+            return 0;
+        if (ai < bi)
+            return -1;
+        if (ai > bi)
+            return 1;
+    }
+    return 0;
+}
 export function corpusDir() {
     return process.env.INTERN_CORPUS_DIR ?? join(homedir(), ".ollama-intern", "corpora");
 }
@@ -36,13 +76,51 @@ export async function loadCorpus(name) {
     if (found !== CORPUS_SCHEMA_VERSION) {
         throw new InternError("SCHEMA_INVALID", `Corpus "${name}" is at schema v${found ?? "unknown"}; this build expects v${CORPUS_SCHEMA_VERSION}. File: ${path}`, `Re-index to upgrade in place: ollama_corpus_index({ name: "${name}", paths: [<your source paths>] }). No migration is performed — the re-index rewrites ${path} with the current schema.`, false);
     }
+    // Refuse to load a corpus that was written by a newer pkg version than
+    // ours. Same schema number, but a newer build may have added fields the
+    // current build would lose on the next write.
+    const writtenBy = parsed.schema_version_written_by;
+    if (typeof writtenBy === "string" && compareVersions(writtenBy, SCHEMA_WRITER_VERSION) > 0) {
+        throw new InternError("SCHEMA_INVALID", `Corpus "${name}" was written by v${writtenBy}; this build is v${SCHEMA_WRITER_VERSION} and refuses to downgrade. File: ${path}`, `Upgrade ollama-intern-mcp to v${writtenBy} or newer, or re-index after downgrading the package deliberately.`, false);
+    }
     return parsed;
 }
 export async function saveCorpus(corpus) {
     assertValidCorpusName(corpus.name);
+    // Refuse to serialize absurdly large corpora — a single JSON.stringify
+    // over 100k+ chunks will hit Node's max string length and OOM.
+    if (corpus.chunks.length > MAX_CHUNKS) {
+        throw new InternError("SCHEMA_INVALID", `Corpus "${corpus.name}" has ${corpus.chunks.length} chunks; cap is ${MAX_CHUNKS}.`, `Split this into multiple smaller corpora (e.g. by directory or topic). A single JSON file this large will blow Node's string-length ceiling on write.`, false);
+    }
     const path = corpusPath(corpus.name);
     await mkdir(dirname(path), { recursive: true });
-    await writeFile(path, JSON.stringify(corpus), "utf8");
+    // Stamp the writer version so older builds can refuse to downgrade.
+    const stamped = { ...corpus, schema_version_written_by: SCHEMA_WRITER_VERSION };
+    const payload = JSON.stringify(stamped);
+    // Observability: payload size in bytes (UTF-8) so ops can spot runaway growth.
+    // Using Buffer.byteLength is accurate for non-ASCII content.
+    // eslint-disable-next-line no-console
+    console.error(`[corpus:save] name=${corpus.name} chunks=${corpus.chunks.length} bytes=${Buffer.byteLength(payload, "utf8")}`);
+    // Atomic write: write to <path>.tmp, fsync, then rename. If Node crashes
+    // mid-write the original file is intact — rename on the same filesystem
+    // is atomic on both POSIX and NTFS.
+    const tmpPath = `${path}.tmp`;
+    const fh = await open(tmpPath, "w");
+    try {
+        await fh.writeFile(payload, "utf8");
+        await fh.sync();
+    }
+    finally {
+        await fh.close();
+    }
+    try {
+        await rename(tmpPath, path);
+    }
+    catch (err) {
+        // Best-effort cleanup of the temp file if rename failed.
+        await unlink(tmpPath).catch(() => { });
+        throw err;
+    }
 }
 export async function listCorpora() {
     const dir = corpusDir();
@@ -78,4 +156,71 @@ export async function listCorpora() {
     summaries.sort((a, b) => a.name.localeCompare(b.name));
     return summaries;
 }
+/**
+ * Fast stale-detection primitive.
+ *
+ * Compares each manifest-declared path's current stat.mtime against the
+ * mtime stored in the corpus's chunks. Returns as soon as any drift is
+ * found — does NOT re-read file contents or re-hash, so it's cheap enough
+ * for callers to poll before deciding whether to pay the full refresh
+ * cost.
+ *
+ * Reasons:
+ *   - "no_corpus"   — corpus JSON missing
+ *   - "no_manifest" — manifest JSON missing
+ *   - "path_missing:<path>"  — manifest declares a path that isn't on disk
+ *   - "path_added:<path>"    — manifest declares a path the corpus has never seen
+ *   - "path_removed:<path>"  — corpus has a path the manifest no longer lists
+ *   - "mtime_drift:<path>"   — file's mtime is later than the corpus record
+ */
+export async function isCorpusStale(name) {
+    assertValidCorpusName(name);
+    let corpus = null;
+    try {
+        corpus = await loadCorpus(name);
+    }
+    catch {
+        // A schema-invalid corpus IS stale (re-index needed).
+        return { stale: true, reason: "no_corpus" };
+    }
+    if (!corpus)
+        return { stale: true, reason: "no_corpus" };
+    const manifest = await loadManifest(name).catch(() => null);
+    if (!manifest)
+        return { stale: true, reason: "no_manifest" };
+    // Build a map path → latest stored mtime from chunks.
+    const storedMtimeByPath = new Map();
+    for (const c of corpus.chunks) {
+        const t = Date.parse(c.file_mtime);
+        if (Number.isNaN(t))
+            continue;
+        const prev = storedMtimeByPath.get(c.path);
+        if (prev === undefined || t > prev)
+            storedMtimeByPath.set(c.path, t);
+    }
+    const manifestSet = new Set(manifest.paths);
+    // Paths in corpus that are no longer declared by the manifest.
+    for (const p of storedMtimeByPath.keys()) {
+        if (!manifestSet.has(p))
+            return { stale: true, reason: `path_removed:${p}` };
+    }
+    for (const p of manifest.paths) {
+        let currentMtime;
+        try {
+            const st = await stat(p);
+            currentMtime = st.mtimeMs;
+        }
+        catch {
+            return { stale: true, reason: `path_missing:${p}` };
+        }
+        const stored = storedMtimeByPath.get(p);
+        if (stored === undefined)
+            return { stale: true, reason: `path_added:${p}` };
+        // Only flag when current is strictly later — allow clock skew that
+        // happens to produce an earlier mtime (e.g. touch to an older date).
+        if (currentMtime > stored + 1)
+            return { stale: true, reason: `mtime_drift:${p}` };
+    }
+    return { stale: false };
+}
 //# sourceMappingURL=storage.js.map