@ruso-0/nreki 11.2.0 → 11.3.1

package/CHANGELOG.md

@@ -2,6 +2,109 @@
 
 All notable changes to NREKI will be documented in this file.
 
+## [11.3.1] - 2026-05-19
+
+### Changed
+
+- **`SYMBOL_REPLACE_LIMIT` default raised 40 L → 100 L.** The legacy 40 L guillotine on `mode:"replace"` was introduced in v9.1 (`3661c31`, 2026-04-13) as a magic number without empirical justification. Phase 1 measurement of 2 880 functions across 5 production TypeScript codebases (NREKI src/, zod, ajv, eventsource, ajv-formats) showed the 40 L cap blocked **10.45% of real-world functions** and **19.06% of NREKI's own source** — a self-inconsistency. The new default (100 L) blocks only 3.02% aggregate (true outliers) and matches NREKI's pre-existing outline auto-expand cutoff (`<=100L` in v10.1.1). The other 10 defense-in-depth gates (anti-sweep shield, kernel TS validation, TTRD, blast radius, Fiedler bridge, Chronos friction, auto-backup, ACID, file lock, topology invalidate) remain unchanged and continue to detect every defect class the size-only gate was incidentally catching.
+- Error message now reports the active threshold and points to the env override:
+  `Blocked: Symbol "X" is 55L (>100L). Use mode:"patch" with search_text and replace_text, or override via NREKI_SYMBOL_LIMIT env.`
+
+### Added
+
+- **`NREKI_SYMBOL_LIMIT` env override** — accepts any integer 1..1000. Parse failures fall back to the default and warn on stderr (never silently disable the gate). Backward-compat: users who prefer the legacy 40 L behavior can set `NREKI_SYMBOL_LIMIT=40`.
+- **`src/limits.ts`** — central, named export `SYMBOL_REPLACE_LIMIT` replaces the magic number `40` in two locations (`src/semantic-edit.ts:637` batch path, `src/semantic-edit.ts:1029` single-edit path).
+- **Empirical analysis docs**:
+  - `docs/threshold-empirical-analysis.md` — methodology, samples, percentile distribution, false-positive rates per threshold (40 / 50 / 60 / 70 / 80 / 100 / 120 / 150).
+  - `docs/furia-threshold-review.md` — adversarial Q1–Q5 review (arbitrariness check, risk surface analysis, ratio-vs-absolute, env-override constraints, legitimate-rewrite scenario).
+  - `scripts/analyze-symbol-sizes.mjs` — reproducible analysis script (TypeScript Compiler API), regenerable on demand.
+- **Tests** — `tests/semantic-edit.test.ts` adds three cases: (a) 55 L symbol is now allowed, (b) 120 L god-function still blocked, (c) error message dynamically reflects active threshold.
+
+### Templates
+
+- `templates/CLAUDE.md`, `templates/AGENTS.md`, `templates/SKILL.md` updated to document the new 100 L default and the `NREKI_SYMBOL_LIMIT` override.
+
+### Migration
+
+- **Existing users:** the only externally-visible change is that symbols 41–100 L now accept `mode:"replace"` where they were previously rejected. No file format change, no API change, no breaking signature. To restore exact pre-v11.3.1 behavior, set `NREKI_SYMBOL_LIMIT=40` in your environment.
+
+## [11.3.0] - 2026-05-19
+
+### Added
+
+- **Agent-aware `nreki init` CLI** — pre-v11.3.0 `nreki init` unconditionally wrote `CLAUDE.md`, `AGENTS.md`, `SKILL.md` plus a Claude Code-specific PreToolUse hook into every project regardless of which AI coding agent the user actually ran. v11.3.0 detects the agent from filesystem signals (`.claude/` / `CLAUDE.md` → claude, `.cursor/` / `.cursorrules` → cursor, `.clinerules` → cline, `.github/copilot-instructions.md` → copilot) and installs only the files that agent reads:
+  - **claude**: `CLAUDE.md`, `SKILL.md`, `.claude/hooks/nreki-enforcer.mjs`, `.claude/settings.json` PreToolUse merge.
+  - **cursor**: `.cursor/rules/nreki.mdc` with `alwaysApply: true` frontmatter.
+  - **cline**: `.clinerules/nreki.md`.
+  - **copilot**: `.github/copilot-instructions.md` (appended if pre-existing).
+  - **generic** (no signal): `AGENTS.md` + an honest disclosure pointing at the `--agent` flag.
+  Flags: `--agent <claude|cursor|cline|copilot|generic>` overrides detection; `--force` rewrites an existing NREKI block; `--dry-run` previews the plan without filesystem writes. The pre-existing NREKI marker check is preserved per file, so `nreki init` remains idempotent.
+- **`tests/cli-init.test.ts`** — 28 filesystem-based tests covering detection priority, all agent install paths, idempotency (marker-based skip), `--force` rewrite, `--dry-run` no-op semantics, and end-to-end auto-detection.
+
+### Changed
+
+- The Claude Code enforcer hook moved from a TypeScript template literal in `src/index.ts` (`getEnforcerScriptContent()`) to a real file at `templates/hooks/nreki-enforcer.mjs`. Template content is read at runtime via `fs.readFileSync`, so future edits to the hook source no longer require navigating nested backslash-escape gymnastics. The runtime behavior of the hook is unchanged.
+- `nreki --help` now documents the `init` subcommand flags.
+
+### Internal
+
+- `src/init/agent-detect.ts` — pure detector returning `{ agent, reason, detected }`.
+- `src/init/init-runner.ts` — orchestrator with `parseInitArgs`, `runInit`, and `formatAction`. Pure functions over the filesystem so tests can `mkdtemp` and assert against on-disk outcomes. The Claude-Code-only `.claude/settings.json` merge is conservative: it preserves user-added PreToolUse matchers and only inserts the ones NREKI owns; malformed JSON aborts the merge with a clear message instead of clobbering the file.
+
+### Migration notes
+
+- Existing Claude Code installs are unaffected: the detector sees their `.claude/` directory and continues to install the same Claude-Code files. Re-running `nreki init` on a v11.2.x Claude Code project will report all four target files as `[skip]` (markers already present).
+- Cursor / Cline / Copilot users on v11.2.x who ran `nreki init` and ended up with stray `CLAUDE.md` / `SKILL.md` files can safely delete them — v11.3.0 will now write the correct agent-specific files for them on the next run.
+
+## [11.2.1] - 2026-05-19
+
+Hot-fix release. v11.2.0 surfaced an EOF-style MCP crash on real-world
+repositories when Claude Code invoked `nreki_navigate action="hybrid_search"`
+(and to a lesser extent `search`, `map`, `orphan_oracle`, `fast_grep`).
+Empirical reproduction via stdio probe in this repo (D:/Nreki, ~12k source
+files, heavy dot-trees `.eval-phase5-cache/` and `.venv-aider/`) showed the
+server never responded inside the client's tool-call timeout window — Claude
+Code surfaced this as `connection closed: calling tools/call: client is closing: EOF`.
+
+### Fixed
+
+- **MCP EOF on first `hybrid_search` / `search` on real repos** — three
+  independent directory walks (NREKI indexer `walkDirectory`, the Phase 5
+  repo-map `walkFiles`, and chokidar's initial scan) used synchronous
+  `fs.readdirSync` and did NOT skip dot-prefixed directories. Heavy
+  dot-trees (`.venv*`, `.cache`, `.turbo`, `.parcel-cache`, `.pytest_cache`,
+  `.mypy_cache`, `.ruff_cache`, `.eval-phase5-cache`, `.nreki-runtime`,
+  etc.) blocked the MCP event loop for tens of seconds to minutes. All
+  three walkers now mirror `BM25Engine.walkSourceFiles`'s policy and skip
+  any dot-prefixed directory.
+- **Watcher initialization no longer blocks server startup** — pre-v11.2.1
+  `await engine.startWatcher()` ran inside `main()` AFTER `server.connect(transport)`,
+  so the MCP transport accepted requests but the watcher's chokidar scan
+  prevented handlers from making forward progress. The watcher now starts
+  in the background; readiness is logged when chokidar emits `ready`.
+- **First-call full-project indexing no longer awaited inside tool
+  handlers** — `hybrid_search`, `search`, `map`, and `orphan_oracle` now
+  kick off `engine.indexDirectory()` in the background via
+  `engine.ensureIndexedBackground()` and return immediately with whatever
+  the current index supports. `hybrid_search` surfaces useful BM25 results
+  on the first call even while NREKI's semantic index warms up; `search`
+  returns a "warming" hint guiding the user to `hybrid_search` / `fast_grep`
+  for an immediate answer. `fast_grep` keeps its existing synchronous
+  bootstrap because the RAM cache contract depends on it.
+- **Defensive `unhandledRejection` / `uncaughtException` handlers** —
+  unexpected async errors no longer terminate the MCP process. Both are
+  logged to stderr (never stdout, which would corrupt JSON-RPC) and the
+  server keeps serving.
+
+### Internal
+
+- `NrekiEngine.ensureIndexedBackground()` coalesces concurrent
+  first-call indexing requests onto a single in-flight promise.
+- chokidar v4 `ignored` option migrated from an array of glob strings
+  (a v3 form not natively interpreted by v4) to a predicate function
+  that combines dot-prefix skipping with the configured glob list via
+  `picomatch.isMatch`.
+
 ## [11.2.0] - 2026-05-18
 
 ### Added

package/README.md

@@ -4,7 +4,7 @@
   <img src="https://img.shields.io/npm/v/@ruso-0/nreki?style=for-the-badge&color=blue" alt="npm version">
   <img src="https://img.shields.io/badge/Tests-783-brightgreen?style=for-the-badge" alt="783 Tests">
   <img src="https://img.shields.io/badge/AHI-9.7%2F10-brightgreen?style=for-the-badge" alt="AHI 9.7/10">
-  <img src="https://img.shields.io/badge/Languages-TS%20%7C%20JS%20%7C%20Go%20%7C%20Python%20%7C%20Kotlin%20%7C%20Java%20%7C%20C%2B%2B-blue?style=for-the-badge" alt="Multi-language">
+  <img src="https://img.shields.io/badge/Languages-TS%20%7C%20JS%20%7C%20Go%20%7C%20Python%20%7C%20Kotlin%20%7C%20Java%20%7C%20C%2B%2B-blue?style=for-the-badge" alt="Multi-language">
   <img src="https://img.shields.io/badge/Cloud-Zero-orange?style=for-the-badge" alt="Zero Cloud">
   <img src="https://img.shields.io/badge/License-Apache_2.0-yellow?style=for-the-badge" alt="Apache 2.0">
 </p>
@@ -24,11 +24,24 @@ claude mcp add nreki -- npx -y @ruso-0/nreki
 # Cursor / any MCP client - add to mcp.json:
 { "mcpServers": { "nreki": { "command": "npx", "args": ["-y", "@ruso-0/nreki"] } } }
 
-# Optional: installs CLAUDE.md instructions + CLI hook firewall
-npx @ruso-0/nreki init
+# Optional: agent-aware instructions install (v11.3.0+)
+npx @ruso-0/nreki init               # auto-detect agent (Claude Code / Cursor / Cline / Copilot / generic)
+npx @ruso-0/nreki init --agent cursor # explicit; valid: claude, cursor, cline, copilot, generic
+npx @ruso-0/nreki init --dry-run     # preview the plan, write nothing
+npx @ruso-0/nreki init --force       # rewrite an existing NREKI block
 ```
 
-First run indexes the project automatically. Zero config for TS/JS; point a `tsconfig.json` at your code and NREKI detects the right validation mode.
+What `nreki init` writes per agent:
+
+| Agent     | Detected via                          | Files installed                                                       |
+|-----------|----------------------------------------|-----------------------------------------------------------------------|
+| `claude`  | `.claude/` or `CLAUDE.md`              | `CLAUDE.md`, `SKILL.md`, `.claude/hooks/nreki-enforcer.mjs`, `.claude/settings.json` |
+| `cursor`  | `.cursor/` or `.cursorrules`           | `.cursor/rules/nreki.mdc` (with `alwaysApply: true` frontmatter)      |
+| `cline`   | `.clinerules` (file or dir)            | `.clinerules/nreki.md`                                                |
+| `copilot` | `.github/copilot-instructions.md`      | `.github/copilot-instructions.md` (appended)                          |
+| `generic` | none of the above                      | `AGENTS.md`                                                           |
+
+First MCP run indexes the project automatically in the background — `hybrid_search` returns BM25 results immediately while NREKI's semantic index warms (v11.2.1+). Zero config for TS/JS; point a `tsconfig.json` at your code and NREKI detects the right validation mode.
 
 ## How it works
 
@@ -53,33 +66,33 @@ Three tools (`nreki_navigate`, `nreki_code`, `nreki_guard`), 23 actions, 4 langu
 - **Defect radar + ghost oracle.** Four inline detectors and a 0-ext-refs tagger run during `outline` - free signals, no extra tool call.
 - **Executable engrams.** Pin insights to symbols. Engrams prefixed `ASSERT` survive AST mutation; everything else invalidates on body change so memory can't go stale.
 
-## Language support (Validation + Auto-heal)
+## Language support (Validation + Auto-heal)
 
 | Language | Validation | Auto-heal |
 |----------|------------|-----------|
 | TypeScript / JavaScript | Full (TS Compiler API) | TS CodeFix API |
-| Go | gopls LSP sidecar | codeAction (atomic) |
-| Python | pyright LSP sidecar | codeAction (atomic) |
-
-## AST parser coverage
-
-NREKI's tree-sitter parser layer indexes additional languages for
-foveal compression + symbol retrieval + semantic-edit syntactic
-validation. These languages do **not** have LSP sidecars and
-therefore receive no auto-heal; otherwise their files participate
-in the retrieval index identically to TypeScript files.
-
-| Language    | Extensions                              | Parser | Foveal | Syntax check | LSP auto-heal | Type Ledger |
-|-------------|-----------------------------------------|--------|--------|--------------|---------------|-------------|
-| TypeScript  | .ts .tsx .mts .cts                      | ✓      | ✓      | ✓            | ✓ (tsc)       | ✓           |
-| JavaScript  | .js .jsx .mjs .cjs                      | ✓      | ✓      | ✓            | ✓ (tsc)       | ✓           |
-| Python      | .py                                     | ✓      | ✓      | ✓            | ✓ (pyright)   | —           |
-| Go          | .go                                     | ✓      | ✓      | ✓            | ✓ (gopls)     | —           |
-| CSS         | .css                                    | ✓      | ✓      | ✓            | —             | —           |
-| JSON        | .json                                   | ✓      | ✓      | ✓            | —             | —           |
-| HTML        | .html                                   | ✓      | ✓      | ✓            | —             | —           |
-| **Kotlin**  | .kt .kts                                | ✓      | ✓      | ✓            | —             | —           |
-| **Java**    | .java                                   | ✓      | ✓      | ✓            | —             | —           |
+| Go | gopls LSP sidecar | codeAction (atomic) |
+| Python | pyright LSP sidecar | codeAction (atomic) |
+
+## AST parser coverage
+
+NREKI's tree-sitter parser layer indexes additional languages for
+foveal compression + symbol retrieval + semantic-edit syntactic
+validation. These languages do **not** have LSP sidecars and
+therefore receive no auto-heal; otherwise their files participate
+in the retrieval index identically to TypeScript files.
+
+| Language    | Extensions                              | Parser | Foveal | Syntax check | LSP auto-heal | Type Ledger |
+|-------------|-----------------------------------------|--------|--------|--------------|---------------|-------------|
+| TypeScript  | .ts .tsx .mts .cts                      | ✓      | ✓      | ✓            | ✓ (tsc)       | ✓           |
+| JavaScript  | .js .jsx .mjs .cjs                      | ✓      | ✓      | ✓            | ✓ (tsc)       | ✓           |
+| Python      | .py                                     | ✓      | ✓      | ✓            | ✓ (pyright)   | —           |
+| Go          | .go                                     | ✓      | ✓      | ✓            | ✓ (gopls)     | —           |
+| CSS         | .css                                    | ✓      | ✓      | ✓            | —             | —           |
+| JSON        | .json                                   | ✓      | ✓      | ✓            | —             | —           |
+| HTML        | .html                                   | ✓      | ✓      | ✓            | —             | —           |
+| **Kotlin**  | .kt .kts                                | ✓      | ✓      | ✓            | —             | —           |
+| **Java**    | .java                                   | ✓      | ✓      | ✓            | —             | —           |
 | **C++**     | .cpp .cc .cxx .hpp .hh .hxx .h*         | ✓      | ✓      | ✓            | —             | —           |
 | **C**       | .c .h*                                  | ✓      | ✓      | ✓            | —             | —           |
 
@@ -90,8 +103,8 @@ broader JVM / native cross-platform ecosystem.
 > *`.h` headers are routed at parse time: headers containing
 > C++ markers (template, namespace, class, `#ifdef __cplusplus`)
 > use the C++ grammar; pure C headers use the C grammar. Default
-> to C grammar for ambiguous cases.
-
+> to C grammar for ambiguous cases.
+
 **Known limitation (v11.0.x):** cross-file import detection for
 Kotlin / Java / C++ / C is not yet implemented. Repo-map dependency edges
 for files in these languages are intra-file only until v11.0.x.1.
@@ -110,14 +123,14 @@ propagate to vendor `wasm/` directory due to skip-if-exists logic in
 **chunks table lacks language column.** Retrieval language-aware scoring
 requires runtime path extension filtering. Breaking migration tracked as
 issue #6 (coordinated with v11.0.2 XML activation due to noise risk
-amplification).
-
-**Type Ledger (cross-file architectural dependency mapping) remains
-TypeScript-specific by design** - it relies on TypeScript compiler-
-derived type information. Multi-language Type Ledger expansion is
-tracked under the Phase 8 roadmap.
-
-## Docs & links
+amplification).
+
+**Type Ledger (cross-file architectural dependency mapping) remains
+TypeScript-specific by design** - it relies on TypeScript compiler-
+derived type information. Multi-language Type Ledger expansion is
+tracked under the Phase 8 roadmap.
+
+## Docs & links
 
 - **[CHANGELOG.md](CHANGELOG.md)** - full version history (every patch, every release, every test count).
 - **[templates/CLAUDE.md](templates/CLAUDE.md)** - optimized instructions auto-installed by `npx @ruso-0/nreki init`.

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

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package/dist/engine/indexer.js

@@ -150,6 +150,17 @@ export class IndexPipeline {
                 const fullPath = path.join(dir, entry.name);
                 const relativePath = path.relative(dirPath, fullPath).replace(/\\/g, "/");
                 if (entry.isDirectory()) {
+                    // v11.2.1: skip dot-prefixed directories (mirrors
+                    // BM25Engine.walkSourceFiles policy at bm25-engine.ts:281).
+                    // Covers .git, .next, .venv*, .eval-phase5-cache, .turbo,
+                    // .cache, .parcel-cache, .pytest_cache, .mypy_cache,
+                    // .ruff_cache, .idea, .vscode, .ipynb_checkpoints, .nreki,
+                    // .nreki-runtime without enumeration. Pre-v11.2.1 these
+                    // were walked synchronously by fs.readdirSync, blocking the
+                    // MCP event loop for tens of seconds on heavy dot-dirs and
+                    // surfacing to Claude Code as a tools/call EOF.
+                    if (entry.name.startsWith("."))
+                        continue;
                     if (!isIgnored(entry.name) && !isIgnored(relativePath) && !isIgnored(relativePath + "/")) {
                         walk(fullPath);
                     }

package/dist/engine/indexer.js.map

@@ -1 +1 @@
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package/dist/engine.d.ts

@@ -61,6 +61,17 @@ export declare class NrekiEngine {
         skipped: number;
         errors: number;
     }>;
+    /**
+     * v11.2.1: kick off a full project index in the background and return
+     * immediately. MCP tool handlers call this on first request so they
+     * can respond inside Claude Code's tool-call timeout window instead
+     * of blocking on a multi-minute walk that surfaces as "connection
+     * closed: EOF" on large repos. Concurrent calls coalesce on the
+     * single in-flight promise; once it settles the next call kicks a
+     * fresh pass (so newly-added trees are eventually picked up).
+     */
+    private backgroundIndexPromise;
+    ensureIndexedBackground(): boolean;
     search(query: string, limit?: number): Promise<import("./engine-types.js").SearchResult[]>;
     /**
      * Lazy-construct the HybridEngine (NREKI semantic + BM25 lexical via RRF).

package/dist/engine.d.ts.map

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

@@ -13,6 +13,7 @@
 import fs from "fs";
 import path from "path";
 import chokidar from "chokidar";
+import picomatch from "picomatch";
 import { NrekiDB } from "./database.js";
 import { estimateTokens } from "./utils/token-estimator.js";
 import { ASTParser } from "./parser.js";
@@ -240,6 +241,33 @@ export class NrekiEngine {
         this.invalidateHybridIndex();
         return result;
     }
+    /**
+     * v11.2.1: kick off a full project index in the background and return
+     * immediately. MCP tool handlers call this on first request so they
+     * can respond inside Claude Code's tool-call timeout window instead
+     * of blocking on a multi-minute walk that surfaces as "connection
+     * closed: EOF" on large repos. Concurrent calls coalesce on the
+     * single in-flight promise; once it settles the next call kicks a
+     * fresh pass (so newly-added trees are eventually picked up).
+     */
+    backgroundIndexPromise = null;
+    ensureIndexedBackground() {
+        if (this.backgroundIndexPromise)
+            return false;
+        if (this.hasIndexedFiles())
+            return false;
+        this.backgroundIndexPromise = this.indexDirectory(this.getProjectRoot())
+            .then((stats) => {
+            logger.info(`Background index complete: ${stats.indexed} indexed, ${stats.skipped} skipped, ${stats.errors} errors.`);
+        })
+            .catch((err) => {
+            logger.error(`Background indexing failed: ${err.message}`);
+        })
+            .finally(() => {
+            this.backgroundIndexPromise = null;
+        });
+        return true;
+    }
     // ─── Search (delegated to SearchEngine) ─────────────────────────
     async search(query, limit = 10) {
         await this.initialize();
@@ -517,8 +545,31 @@ export class NrekiEngine {
         if (this.watcher)
             return this.watcherReady ?? Promise.resolve();
         const shouldWatchFile = (fp) => this.config.extensions.includes(path.extname(fp).toLowerCase());
+        // v11.2.1: combine the configured globs with a dot-prefix predicate so
+        // chokidar's initial scan does not enumerate heavy dot-directories
+        // (.venv*, .eval-phase5-cache, .turbo, .cache, .parcel-cache,
+        // .pytest_cache, .nreki-runtime, etc.) Pre-v11.2.1 the watcher walked
+        // these synchronously during scan, holding the event loop and surfacing
+        // to MCP tool callers as an EOF crash.
+        const ignoredGlobs = this.config.ignorePaths;
+        const ignoredMatcher = (filePath) => {
+            const base = path.basename(filePath);
+            if (base.startsWith(".")) {
+                // Always allow the project root itself even if it sits inside
+                // a dot-path the user explicitly chose to watch.
+                const isWatchRoot = this.config.watchPaths.some(w => path.resolve(w) === path.resolve(filePath));
+                if (!isWatchRoot)
+                    return true;
+            }
+            // Defer to the configured glob list for the remaining ignores.
+            for (const g of ignoredGlobs) {
+                if (picomatch.isMatch(filePath, g))
+                    return true;
+            }
+            return false;
+        };
         this.watcher = chokidar.watch(this.config.watchPaths, {
-            ignored: this.config.ignorePaths,
+            ignored: ignoredMatcher,
             persistent: true,
             ignoreInitial: true, // prevent race with handler bootstrap
         });

package/dist/engine.js.map

@@ -1 +1 @@
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package/dist/handlers/navigate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"navigate.d.ts","sourceRoot":"","sources":["../../src/handlers/navigate.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,OAAO,KAAK,EAAE,eAAe,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAC;AAmBxF,wBAAsB,YAAY,CAC9B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA6F1B;AAID,wBAAsB,gBAAgB,CAClC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAoF1B;AAID,wBAAsB,gBAAgB,CAClC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAiD1B;AAgDD,wBAAsB,aAAa,CAC/B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAuL1B;AAID,wBAAsB,SAAS,CAC3B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAgC1B;AAmCD,wBAAsB,qBAAqB,CACvC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA8H1B;AAID,wBAAsB,kBAAkB,CACpC,OAAO,EAAE,cAAc,EACvB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAgH1B;AAID,wBAAsB,eAAe,CACjC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAiD1B;AAID;;;;;;;;;;;;;GAaG;AACH,wBAAsB,kBAAkB,CACpC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAqG1B;AAED;;;;;;;;GAQG;AACH,wBAAsB,cAAc,CAChC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA+F1B"}
+{"version":3,"file":"navigate.d.ts","sourceRoot":"","sources":["../../src/handlers/navigate.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,OAAO,KAAK,EAAE,eAAe,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAC;AAmBxF,wBAAsB,YAAY,CAC9B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA2G1B;AAID,wBAAsB,gBAAgB,CAClC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAoF1B;AAID,wBAAsB,gBAAgB,CAClC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAiD1B;AAgDD,wBAAsB,aAAa,CAC/B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAuL1B;AAID,wBAAsB,SAAS,CAC3B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAkC1B;AAmCD,wBAAsB,qBAAqB,CACvC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA8H1B;AAID,wBAAsB,kBAAkB,CACpC,OAAO,EAAE,cAAc,EACvB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAkH1B;AAID,wBAAsB,eAAe,CACjC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CAiD1B;AAID;;;;;;;;;;;;;GAaG;AACH,wBAAsB,kBAAkB,CACpC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA2G1B;AAED;;;;;;;;GAQG;AACH,wBAAsB,cAAc,CAChC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,kBAAkB,GACzB,OAAO,CAAC,eAAe,CAAC,CA+F1B"}

package/dist/handlers/navigate.js

@@ -21,13 +21,26 @@ export async function handleSearch(params, deps) {
     const { engine } = deps;
     await engine.initialize();
     const query = params.query ?? "";
-    if (!engine.hasIndexedFiles()) {
-        logger.info("First-time project indexing — this may take a moment for large repos.");
-        await engine.indexDirectory(engine.getProjectRoot());
-    }
+    // v11.2.1: non-blocking lazy index. Pre-v11.2.1 this awaited a full
+    // walk that exceeded Claude Code's tool-call timeout on large repos
+    // and surfaced as EOF. The handler now returns early with a hint when
+    // the index is still warming; subsequent calls progressively gain
+    // coverage. fast_grep / hybrid_search remain usable in the meantime.
+    const indexStarted = !engine.hasIndexedFiles() && engine.ensureIndexedBackground();
     const limit = typeof params.limit === "number" ? Math.min(50, Math.max(1, params.limit)) : 10;
     const include_raw = params.include_raw === true;
     const results = await engine.search(query, limit);
+    if (indexStarted && results.length === 0) {
+        return {
+            content: [{
+                    type: "text",
+                    text: `Index pending for: "${query}"\n\n` +
+                        `NREKI's semantic index is warming in the background. Try again in a few seconds, ` +
+                        `or use action:"hybrid_search" (BM25-backed, no wait) or action:"fast_grep" ` +
+                        `(exact substring) for immediate results.`,
+                }],
+        };
+    }
     if (results.length === 0) {
         return {
             content: [{
@@ -455,9 +468,11 @@ export async function handleOutline(params, deps) {
 export async function handleMap(params, deps) {
     const { engine } = deps;
     await engine.initialize();
+    // v11.2.1: kick off indexing in the background instead of awaiting it
+    // — the repo map renders from whatever is already in the DB and the
+    // next call picks up the freshly-indexed entries.
     if (!engine.hasIndexedFiles()) {
-        logger.info("First-time project indexing — this may take a moment for large repos.");
-        await engine.indexDirectory(engine.getProjectRoot());
+        engine.ensureIndexedBackground();
     }
     const refresh = params.refresh === true;
     const { text: cachedText, map } = await engine.getRepoMap(refresh);
@@ -619,9 +634,11 @@ export async function handlePrepareRefactor(params, deps) {
 export async function handleOrphanOracle(_params, deps) {
     const { engine } = deps;
     await engine.initialize();
+    // v11.2.1: non-blocking lazy index. orphan_oracle reads whatever is
+    // already in the repo map; if the index is warming, the answer may be
+    // incomplete on this call but the next call will see new entries.
     if (!engine.hasIndexedFiles()) {
-        logger.info("First-time project indexing — this may take a moment for large repos.");
-        await engine.indexDirectory(engine.getProjectRoot());
+        engine.ensureIndexedBackground();
     }
     const { map } = await engine.getRepoMap();
     const graph = await engine.getDependencyGraph();
@@ -787,9 +804,15 @@ export async function handleHybridSearch(params, deps) {
             isError: true,
         };
     }
-    if (!engine.hasIndexedFiles()) {
-        logger.info("First-time project indexing for hybrid_search...");
-        await engine.indexDirectory(engine.getProjectRoot());
+    // v11.2.1: do NOT block on a full indexDirectory walk. On large repos
+    // that walk takes longer than Claude Code's tool-call timeout and
+    // surfaces as "connection closed: EOF". BM25 carries its own walker
+    // and can serve lexical results even while NREKI's semantic index
+    // populates in the background. Subsequent calls progressively gain
+    // semantic coverage.
+    const indexStarted = !engine.hasIndexedFiles() && engine.ensureIndexedBackground();
+    if (indexStarted) {
+        logger.info("hybrid_search: NREKI index pending; BM25 results only this call.");
     }
     const topK = typeof params.limit === "number" ? Math.min(20, Math.max(1, params.limit)) : 10;
     const hybrid = await engine.getHybridEngine();