@nanonets/graft 0.9.1 → 0.10.0

package/README.md

@@ -5,6 +5,7 @@
 ### Turbocharge Claude Code, Cursor, Codex, Gemini & every coding agent: faster, cheaper, with contextual understanding specific to your codebase.
 
 <p>
+  <a href="https://github.com/NanoNets/Graft"><img src="https://img.shields.io/github/stars/NanoNets/Graft?style=for-the-badge&logo=github&logoColor=white&label=Star%20on%20GitHub&color=FFC83D" /></a>
   <a href="https://graft.nanonets.ai"><img src="https://img.shields.io/badge/website-graft.nanonets.ai-546FFF?style=for-the-badge" /></a>
   <a href="https://discord.gg/zxmKweAA29"><img src="https://img.shields.io/badge/Discord-join-5865F2?style=for-the-badge&logo=discord&logoColor=white" /></a>
   <a href="https://www.npmjs.com/package/@nanonets/graft"><img src="https://img.shields.io/npm/v/%40nanonets%2Fgraft?style=for-the-badge&logo=npm&logoColor=white&label=npm" /></a>
@@ -20,17 +21,17 @@
 
 | Metric | Cold Claude Code | Claude Code with graft |
 |---|---|---|
-| Tool-call savings | Baseline | **+46%** |
+| Tool-call reduction | Baseline | **+46%** |
 | Token savings | Baseline | **+42%** |
 | Time savings | Baseline | **+60%** |
 | Correctness | 54% | **66% (+12 pts)** |
 
-<sub>Efficiency is a 162-run controlled benchmark (same agent, same file tools, only the context differs). Correctness is **SWE-bench Verified**, graded by the official harness — graft resolved 66% of instances tested against Cold Claude Code's 54%. The "up to 4× cheaper / 3× faster" figures are the biggest single-task wins from a separate real-repo sweep (PocketBase, ollama, Excalidraw). [Efficiency method ↓](#benchmark) · [SWE-bench ↓](#swe-bench-verified) · [Per-repo numbers ↓](#tested-on-your-popular-repos)</sub>
+<sub>Efficiency is a 162-run controlled benchmark (same agent, same file tools, only the context differs). Correctness is **SWE-bench Verified**, graded by the official harness — graft resolved 66% of instances tested against Cold Claude Code's 54%. [Efficiency method ↓](#benchmark) · [SWE-bench ↓](#swe-bench-verified) · [Per-repo numbers ↓](#tested-on-your-popular-repos)</sub>
 
 </div>
 
 <p align="center">
-  <img src="assets/graft-terminal.png" alt="Two commands — npm install and graft init — then Graft rides along in a Claude Code session, statusline synced" width="820"/>
+  <img src="assets/graft-comparison-demo.gif" alt="Side-by-side comparison of a coding agent working with and without graft" width="820"/>
 </p>
 
 ---
@@ -43,6 +44,7 @@
 - [Benchmark](#benchmark)
 - [SWE-bench Verified](#swe-bench-verified)
 - [How the graph gets built](#how-the-graph-gets-built)
+- [Supported languages](#supported-languages)
 - [What's in a node](#whats-in-a-node)
 - [What runs where](#what-runs-where)
 - [Agent integration](#agent-integration) — [MCP server](#mcp-server) · [Claude Code (deep integration)](#claude-code-deep-integration)
@@ -75,6 +77,10 @@ git add .claude && git commit -m "wire in graft"
 
 Prefer not to install globally? `npx @nanonets/graft init` works the same way.
 
+<p align="center">
+  <img src="assets/graft-terminal.png" alt="Two commands — npm install and graft init — then Graft rides along in a Claude Code session, statusline synced" width="820"/>
+</p>
+
 ---
 
 ## The problem
@@ -147,48 +153,6 @@ The sweep above is our harness measuring our mechanism. So we ran the industry-s
 | API-request savings | 2,455 | **1,875** | **+24%** |
 | Wall-clock savings | 13,094s | **8,922s** | **+32%** |
 
-### Where graft fixed what cold missed
-
-| SWE-bench instance | Cold Claude Code | Claude Code with graft | Token usage vs. cold | Tool usage vs. cold |
-|---|---|---|---:|---:|
-| `django-11532` | Failed: 131 / 149 tests | **Passed: 149 / 149 tests** | **63%** | **60%** |
-| `django-16263` | Failed: 102 / 103 tests | **Passed: 103 / 103 tests** | **51%** | **74%** |
-| `sphinx-9461` | Failed: 61 / 62 tests | **Passed: 62 / 62 tests** | **91%** | **88%** |
-| `django-11400` | Failed: 62 / 64 tests | **Passed: 64 / 64 tests** | 347% | 308% |
-| `pylint-6386` | Failed: 7 / 8 tests | **Passed: 8 / 8 tests** | 163% | 132% |
-| `django-11885` | Failed: 42 / 44 tests | **Passed: 44 / 44 tests** | 219% | 172% |
-| `pytest-5840` | Failed: 51 / 53 tests | **Passed: 53 / 53 tests** | **30%** | **39%** |
-| `sphinx-8548` | Failed: 5 / 6 tests | **Passed: 6 / 6 tests** | **83%** | **80%** |
-| `django-12406` | Failed: 166 / 168 tests | **Passed: 168 / 168 tests** | 125% | 103% |
-| `django-16938` | Failed: 83 / 88 tests | **Passed: 88 / 88 tests** | 154% | 119% |
-
-### Where graft cut the cost
-
-| SWE-bench instance | Cold Claude Code | Claude Code with graft | Token usage vs. cold | Tool usage vs. cold |
-|---|---|---|---:|---:|
-| `sphinx-10673` | Passed: 10 / 10 tests | **Passed: 10 / 10 tests** | **50%** | **51%** |
-| `django-16263` | Failed: 102 / 103 tests | **Passed: 103 / 103 tests** | **51%** | **74%** |
-| `django-11276` | Passed: 574 / 574 tests | **Passed: 574 / 574 tests** | **61%** | **58%** |
-| `django-10554` | Passed: 25 / 25 tests | **Passed: 25 / 25 tests** | **66%** | **69%** |
-| `django-11133` | Passed: 65 / 65 tests | **Passed: 65 / 65 tests** | **78%** | **61%** |
-| `sphinx-9461` | Failed: 61 / 62 tests | **Passed: 62 / 62 tests** | **91%** | **88%** |
-| `matplotlib-14623` | Passed: 401 / 401 tests | **Passed: 401 / 401 tests** | **95%** | **89%** |
-| `matplotlib-25775` | Passed: 96 / 96 tests | **Passed: 96 / 96 tests** | **98%** | **80%** |
-| `pytest-5840` | Failed: 51 / 53 tests | **Passed: 53 / 53 tests** | **30%** | **39%** |
-| `django-12741` | Passed: 69 / 69 tests | **Passed: 69 / 69 tests** | **47%** | **42%** |
-| `sympy-19783` | Passed: 11 / 11 tests | **Passed: 11 / 11 tests** | **61%** | **64%** |
-| `pylint-8898` | Passed: 19 / 19 tests | **Passed: 19 / 19 tests** | **62%** | **67%** |
-| `pylint-6528` | Passed: 175 / 175 tests | **Passed: 175 / 175 tests** | **67%** | **71%** |
-| `sklearn-12682` | Passed: 67 / 67 tests | **Passed: 67 / 67 tests** | **72%** | **70%** |
-| `xarray-3993` | Passed: 2400 / 2400 tests | **Passed: 2400 / 2400 tests** | **74%** | **65%** |
-| `xarray-3305` | Passed: 654 / 654 tests | **Passed: 654 / 654 tests** | **77%** | **70%** |
-| `sphinx-8548` | Failed: 5 / 6 tests | **Passed: 6 / 6 tests** | **83%** | **80%** |
-| `django-16315` | Passed: 43 / 43 tests | **Passed: 43 / 43 tests** | **85%** | **83%** |
-| `django-16032` | Passed: 79 / 79 tests | **Passed: 79 / 79 tests** | **90%** | **91%** |
-| `django-14011` | Passed: 19 / 19 tests | **Passed: 19 / 19 tests** | **90%** | **96%** |
-| `sphinx-8120` | Passed: 45 / 45 tests | **Passed: 45 / 45 tests** | **93%** | **75%** |
-| `django-15103` | Passed: 19 / 19 tests | **Passed: 19 / 19 tests** | **96%** | **80%** |
-
 graft resolved **33 of 50 instances** against Cold Claude Code's 27 — and got there with 25% fewer tool calls, 23% fewer tokens, and 32% less wall-clock time. Every correctness win has the same shape: the baseline patches one file and misses its siblings. On `django-11532` it patched 1 of the 5 files the fix requires and broke 18 previously-passing tests, twice over. On `django-16263` it patched 1 of 4 and scored 102 / 103. graft found the rest — and on `django-16263` did it in half the tokens and half the time.
 
 Two harnesses, two claims: the controlled sweep says graft is cheaper and faster, SWE-bench says it's also more correct.
@@ -221,6 +185,32 @@ Alongside the markdown graph, `graft build` builds `graft/.graph/wiring.json`
 
 ---
 
+## Supported languages
+
+Graft parses with tree-sitter at two levels of fidelity, plus an optional
+compiler-grade layer — all `$0` and deterministic (no model, no key):
+
+- **Full-fidelity** — hand-written extractors with scope-aware, cross-file call
+  and import resolution:
+  **TypeScript / JavaScript** (incl. JSX & TSX), **Python**, **Go**.
+
+- **Broad** — symbols (functions, classes, methods, types, …) plus name-resolved
+  call edges via a generic tree-sitter extractor, one grammar per language:
+  **Rust, Java, C, C++, C#, Ruby, PHP, Kotlin, Scala, Swift, Elixir, Solidity,
+  OCaml, Zig, Dart**.
+
+- **Compiler-grade edges (opt-in)** — `graft build --lsp` adds precise
+  `lsp_resolved` call edges (member calls the static pass can't type) when a
+  language server is on your `PATH`: **rust-analyzer** (Rust), **clangd** (C/C++),
+  **gopls** (Go), **pyright** (Python), **typescript-language-server** (TS/JS).
+  It's best-effort — with no server installed the graph is unchanged.
+
+Twenty languages in total. A file whose language isn't listed is skipped, not
+indexed. Adding a broad-tier language is a small contribution — see
+[CREDITS.md](CREDITS.md) for the folks who added the current set.
+
+---
+
 ## What's in a node
 
 A node is a single markdown file. Most code maps stop at an address: this thing lives in that file, on that line. That tells an agent where to look, not what it will find, so it still has to open the source and read. A Graft node holds the meaning inline, so the agent learns what it needs up front and opens the file only when it wants more.
@@ -320,6 +310,11 @@ Where a CLI agent supports user-level `hooks.json`, `init` also installs Graft's
 - **auto-sync** — every graft query brings the graph up to date first, so an answer always describes the code as it is right now, uncommitted edits included. A query refreshes only what it reads; the markdown under `graft/` is refreshed by the background rebuild at the end of a turn that touched code. Both are structural and `$0` — auto-sync never calls the LLM on its own
 - **context on tap** — each prompt pulls the matching nodes into the session; editing a file surfaces what depends on it ("blast radius"); new sessions start with the repo map
 
+<p align="center">
+  <img src="assets/graft-hooks-demo.gif" alt="How Claude Code hooks wire graft in: install, graft init, then the hooks loop (session start, user prompt, post tool use, stop) keeps the graph built, read, and committed automatically" width="820"/>
+  <br/><sub>install → init → hooks keep the graph fresh every session</sub>
+</p>
+
 <p align="center">
   <img src="assets/graft-hook-blast-radius-demo.gif" alt="graft's post-edit hook: editing node-file.ts prints its blast radius (who depends on it) inline, the statusline flips stale → syncing → synced on its own, and the same dependents light up in graft viz" width="820"/>
   <br/><sub>edit a file → blast radius appears inline → graph auto-resyncs → confirmed in <code>graft viz</code></sub>
@@ -438,6 +433,15 @@ Graft handles two shapes without any config:
 Either way, narrow to one sub-project with `graft ask "<task>" --in <scope>/`
 once you know where you're working.
 
+`graft init` at the parent of a multi-repo folder wires **every child repo too**,
+not just the parent — an agent session opens at a repo root and reads its
+instruction files from there, so each child needs its own. A session started in
+the parent gets the federated view; one started in a child sees that repo alone.
+
+Commands also find the graph from a subdirectory: with no `[dir]` argument they
+walk up to the nearest `graft/`, so `graft ask` works from `src/deep/inside/`
+without a `cd` to the repo root.
+
 ## Visualize it (`graft viz`)
 
 `graft viz` opens a local, interactive view of both graphs — no install, no dev

package/dist/ask/fuse.d.ts.map

@@ -1 +1 @@
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package/dist/ask/fuse.js

@@ -166,25 +166,44 @@ export function rankScopesAndFuse(scopes, ops, graphWeight, rescueFloor) {
     }
     const alsoMatched = [];
     const scoped = [];
+    // Per-scope raw best + strength, computed once so we can pick survivors and,
+    // if the gate would exclude EVERY scope, rescue the strongest one (below).
+    const meta = new Map();
     for (const [scope, lex] of lexByScope) {
-        // Raw best (+ its doc id) for THIS scope, score desc / id asc — same
-        // tiebreak fuseScopes uses, so the reported bestId is deterministic.
-        let maxLex = 0;
-        let bestId = "";
-        for (const [id, v] of lex) {
+        let maxLex = 0, bestId = "";
+        for (const [id, v] of lex)
             if (v > maxLex || (v === maxLex && id < bestId)) {
                 maxLex = v;
                 bestId = id;
             }
-        }
         if (maxLex <= 0)
-            continue; // no positive-scoring doc — contributes nothing
+            continue;
         const { coverage, coverageStrong } = ops.strength(scope, bestId);
-        if (coverageStrong < STRONG_FLOOR && coverage < HIGH_FLOOR) {
-            alsoMatched.push({ scope, bestId });
-            continue; // excluded from fusion — no walk, no blend
-        }
-        // Pass 2: only surviving scopes pay for the graph walk + blend.
+        // strength is the scale-INVARIANT [0,1] match share (name vs name+path+body);
+        // used to pick the rescue scope fairly across corpora, unlike raw maxLex.
+        meta.set(scope, { lex, maxLex, bestId, strength: Math.max(coverage, coverageStrong), passes: coverageStrong >= STRONG_FLOOR || coverage >= HIGH_FLOOR });
+    }
+    const survivors = [...meta.entries()].filter(([, m]) => m.passes).map(([s]) => s);
+    // Anti-abstain rescue: the strength gate is a SHARE of the whole query, so a
+    // long/verbose query (a pasted issue body) can push every scope below the
+    // floor and make `ask` return nothing — measurably worse than grep. When the
+    // gate would exclude every scope yet real matches exist, keep the single
+    // strongest scope so `ask` returns best-effort hits (the escalation nudge
+    // already tells the agent to switch to grep if they look weak) instead of
+    // abstaining. The gate still does its real job — suppressing a weak scope
+    // beside a strong one — whenever any scope passes.
+    if (survivors.length === 0 && meta.size > 0) {
+        // Tiebreak on scale-invariant match STRENGTH (not raw per-corpus maxLex,
+        // which would let the biggest scope's numerically-larger score win — the very
+        // cross-corpus scale bias RRF exists to avoid). Fall back to maxLex only when
+        // strength ties (e.g. all zero), then scope name for determinism.
+        survivors.push([...meta.entries()].sort((a, b) => b[1].strength - a[1].strength || b[1].maxLex - a[1].maxLex || a[0].localeCompare(b[0]))[0][0]);
+    }
+    for (const [scope, m] of meta)
+        if (!survivors.includes(scope))
+            alsoMatched.push({ scope, bestId: m.bestId });
+    for (const scope of survivors) {
+        const { lex, maxLex } = meta.get(scope);
         const pr = ops.walk(scope, lex);
         const candidates = new Set(lex.keys());
         for (const [id, p] of pr)
@@ -192,8 +211,7 @@ export function rankScopesAndFuse(scopes, ops, graphWeight, rescueFloor) {
                 candidates.add(id);
         for (const id of candidates) {
             const lexN = maxLex > 0 ? (lex.get(id) ?? 0) / maxLex : 0;
-            const blended = (lexN + graphWeight * (pr.get(id) ?? 0)) *
-                (ops.rankFactor?.(scope, id) ?? 1);
+            const blended = (lexN + graphWeight * (pr.get(id) ?? 0)) * (ops.rankFactor?.(scope, id) ?? 1);
             if (blended > 0)
                 scoped.push({ id, scope, score: blended });
         }

package/dist/ask/fuse.js.map

@@ -1 +1 @@
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package/dist/claude/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/claude/init.ts"],"names":[],"mappings":"AAOA,OAAO,EAA6B,KAAK,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClF,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAErD;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,YAAY,EAAE,CAWzD;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,OAAO,CASrG;AAED,MAAM,WAAW,UAAU;IACzB,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,8EAA8E;IAC9E,GAAG,EAAE,QAAQ,CAAC;IACd,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,KAAK,EAAE,OAAO,CAAC;CAChB;AAED,wBAAgB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAO,GAAG,UAAU,CA+BjG"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/claude/init.ts"],"names":[],"mappings":"AAOA,OAAO,EAA6B,KAAK,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAElF,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAErD;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,YAAY,EAAE,CAWzD;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,OAAO,CAWrG;AAED,MAAM,WAAW,UAAU;IACzB,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,8EAA8E;IAC9E,GAAG,EAAE,QAAQ,CAAC;IACd,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,KAAK,EAAE,OAAO,CAAC;CAChB;AAED,wBAAgB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAO,GAAG,UAAU,CA+BjG"}

package/dist/claude/init.js

@@ -1,4 +1,4 @@
-import { mkdirSync, writeFileSync, readFileSync, existsSync, chmodSync } from 'node:fs';
+import { mkdirSync, writeFileSync, readFileSync, chmodSync } from 'node:fs';
 import { join, dirname } from 'node:path';
 import { execFileSync } from 'node:child_process';
 import { mergeGraftSettings } from './settings-merge.js';
@@ -6,6 +6,7 @@ import { statuslineShim, hooksShim } from './shim-template.js';
 import { skillTemplate } from './skill-template.js';
 import { claudeDistDir } from './paths.js';
 import { mergeJsonKey, serverEntry } from '../hosts/mcp-config.js';
+import { hasGraftIndex } from '../graph/root.js';
 /**
  * The files `runInit` writes — pure, no writes, so `--dry-run` and the picker
  * can report them up front. All repo-local: the Claude Code layer never writes
@@ -29,8 +30,10 @@ export function claudeTargets(dir) {
  * Best-effort; the user can always run `graft build` (the epilogue says so).
  */
 export function buildGraphIfMissing(dir, opts) {
-    const wiring = join(dir, 'graft', '.graph', 'wiring.json');
-    if (opts.build === false || !opts.cliPath || existsSync(wiring))
+    // `hasGraftIndex`, not just wiring.json: a workspace parent's graph IS its
+    // `workspace.json` (nodes live in the children), so testing for wiring.json
+    // alone would call it unbuilt and rebuild every child on each init.
+    if (opts.build === false || !opts.cliPath || hasGraftIndex(dir))
         return false;
     try {
         execFileSync(process.execPath, [opts.cliPath, 'build', '.'], { cwd: dir, stdio: 'inherit', timeout: 300000 });

package/dist/claude/init.js.map

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

@@ -6,7 +6,7 @@
  */
 import "dotenv/config";
 import { Command } from "commander";
-import { relative, resolve } from "node:path";
+import { join, relative, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
 import { Graft } from "./engine.js";
 import { resolveConfig } from "./ai/providers.js";
@@ -19,6 +19,8 @@ import { contextDirFor } from "./context/node-file.js";
 import { loadGraphCached } from "./graph/load.js";
 import { ensureFreshChildren, ensureFreshGraph, refreshNote } from "./graph/refresh.js";
 import { isWorkspaceBuildRoot, readWorkspace } from "./graph/workspace.js";
+import { nearestGraftRoot } from "./graph/root.js";
+import { discoverWorkspaceChildren } from "./graph/scopes.js";
 import { runWorkspaceAsk, runWorkspaceBuild, runWorkspaceCallers, runWorkspaceCheck, runWorkspaceGrep, runWorkspaceMap, } from "./graph/workspace-cli.js";
 import { formatInitEpilogue } from "./cli-epilogue.js";
 import { planInit, selectedWrites } from "./hosts/plan.js";
@@ -49,6 +51,22 @@ function cliConfig() {
     };
 }
 const engineFrom = () => new Graft(cliConfig());
+/** Text for the omitted-`[dir]` case, shared by every query command's help. */
+const DIR_ARG = ["[dir]", "repository root (default: nearest ancestor with a graft/ index)"];
+/**
+ * The root a query runs against: the dir the user named, else the nearest
+ * ancestor holding a graft index (`graph/root.ts`) so a shell or agent session
+ * in a subdirectory still finds the graph. The walk is announced on stderr —
+ * answering from an ancestor's graph must never be silent.
+ */
+function queryRoot(dir) {
+    if (dir !== undefined)
+        return resolve(dir);
+    const { root, levels } = nearestGraftRoot(process.cwd(), program.opts().dir);
+    if (levels > 0)
+        console.error(`[graft] no graft/ here — answering from ${root}/graft`);
+    return root;
+}
 /**
  * Bring the graph up to date with the working tree before a query answers from it
  * — the same gate the MCP tools run (see `graph/refresh.ts`). Cheap when nothing
@@ -95,6 +113,7 @@ program
     .option("-e, --extensions <exts...>", 'code extensions to include (e.g. ".ts" ".py")')
     .option("-j, --concurrency <n>", "files summarized in parallel during --deep (default 5)")
     .option("--no-reuse", "re-parse every file instead of replaying unchanged ones from the extraction cache")
+    .option("--lsp", "add compiler-grade call edges via a language server if one is installed (opt-in, slower; e.g. rust-analyzer, clangd)")
     .option("--include-dir <name>", "override SKIP_DIRS for this repo's walks — repeatable (e.g. --include-dir build --include-dir tools); " +
     "persisted, so a later build (and the hooks/refresh path) include it without the flag; dot-dirs are never overridable", (val, prev) => [...prev, val], [])
     .action(async (dir, opts) => {
@@ -171,6 +190,7 @@ program
         llm: deep,
         concurrency,
         reuse: opts.reuse,
+        lsp: opts.lsp,
         onProgress: ({ phase, index, total, file }) => process.stderr.write(`\r${phase === "enrich" ? "summarizing" : "parsing"} ${index + 1}/${total}: ${file.slice(0, 50).padEnd(50)}`),
     });
     process.stderr.write("\n");
@@ -193,18 +213,20 @@ program
     .command("ask")
     .description("Query the graft/ graph — returns ranked nodes + exact file:line, routed to prose or wiring ($0, no key)")
     .argument("<query>", "what you want to understand, in plain words")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("-n, --limit <n>", "max results", "8")
     .option("--source", "inline the source at each file:line hit (retriever mode — the pack IS the answer, no need to re-open files)")
     .option("--full", "with --source: inline whole definition spans instead of the default ≤8-line crux excerpts")
     .option("--in <path>", "narrow to nodes under this path prefix, filtered before scoring (segment-aware, like scopeOf)")
     .option("--json", "output the result as JSON")
+    .option("--no-graph-rank", "rank by lexical relevance only, without the graph-connectivity re-rank (ablation/eval)")
     .option(...NO_REFRESH_FLAG)
-    .action(async (query, dir, opts) => {
+    .action(async (query, dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     await refreshBefore(dir, opts);
     const askGlobalDir = program.opts().dir;
-    if (readWorkspace(resolve(dir), askGlobalDir)) {
-        runWorkspaceAsk(resolve(dir), askGlobalDir, query, {
+    if (readWorkspace(dir, askGlobalDir)) {
+        runWorkspaceAsk(dir, askGlobalDir, query, {
             limit: Number(opts.limit), source: opts.source, full: opts.full, in: opts.in, json: opts.json,
         });
         return;
@@ -212,7 +234,7 @@ program
     const engine = engineFrom();
     let r;
     try {
-        r = engine.ask(dir, query, { limit: Number(opts.limit), source: opts.source, full: opts.full, in: opts.in });
+        r = engine.ask(dir, query, { limit: Number(opts.limit), source: opts.source, full: opts.full, in: opts.in, graphRank: opts.graphRank });
     }
     catch (err) {
         console.error(`✗ ${err instanceof Error ? err.message : String(err)}`);
@@ -231,10 +253,11 @@ program
     .command("skeleton")
     .description("Signatures-only view of one file from the wiring graph — the cheapest way to see a file's API surface")
     .argument("<file>", "repo-relative path (or unique basename) of the file")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("--json", "output the result as JSON")
     .option(...NO_REFRESH_FLAG)
-    .action(async (file, dir, opts) => {
+    .action(async (file, dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     await refreshBefore(dir, opts);
     const { skeleton, formatSkeleton } = await import("./ask/ask.js");
     const globalOpts = program.opts();
@@ -247,18 +270,19 @@ program
 program
     .command("check")
     .description("Fail if graft/ is stale relative to the code (for CI)")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("-e, --extensions <exts...>", "code extensions to include")
     .option("--json", "output the drift as JSON")
-    .action((dir, opts) => {
+    .action(async (dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     const checkGlobalDir = program.opts().dir;
-    if (readWorkspace(resolve(dir), checkGlobalDir)) {
-        runWorkspaceCheck(resolve(dir), checkGlobalDir);
+    if (readWorkspace(dir, checkGlobalDir)) {
+        await runWorkspaceCheck(dir, checkGlobalDir);
         return;
     }
     const engine = engineFrom();
     const r = engine.check(dir, { extensions: opts.extensions });
-    const g = engine.checkGraph(dir); // graph.json is only judged when it exists
+    const g = await engine.checkGraph(dir); // graph.json is only judged when it exists
     // A layer that IS present must be in sync; a never-built layer (keyless
     // build skips the markdown layer) is informational, not a failure.
     const bothMissing = r.missing && g.missing;
@@ -286,10 +310,11 @@ program
 program
     .command("viz")
     .description("Serve an interactive visualization of the context graph (and graph.json when present)")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("-p, --port <port>", "port to serve on", "4400")
     .option("--no-open", "don't open the browser")
-    .action(async (dir, opts) => {
+    .action(async (dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     const { existsSync } = await import("node:fs");
     const { resolve, basename } = await import("node:path");
     const { spawn } = await import("node:child_process");
@@ -319,28 +344,29 @@ program
 program
     .command("mcp")
     .description("Serve the graph over MCP (stdio) — exposes graft_find_code, graft_trace_calls, graft_find_all, graft_file_api, graft_repo_map and graft_check_freshness as tools")
-    .argument("[dir]", "repository root", ".")
-    .action(async (dir) => {
-    const { resolve } = await import("node:path");
+    .argument(...DIR_ARG)
+    .action(async (dirArg) => {
+    const dir = queryRoot(dirArg);
     const { startMcpServer } = await import("./mcp/server.js");
     const globalOpts = program.opts();
-    startMcpServer(resolve(dir), globalOpts.dir, currentVersion);
+    startMcpServer(dir, globalOpts.dir, currentVersion);
 });
 program
     .command("callers")
     .description("Who calls/references a symbol ($0, no LLM). --direction out gives callees (what it calls); --depth N (or all) walks transitively for full blast radius")
     .argument("<symbol>", "bare name, qualified (Class.method), or package-qualified (pkg.Fn)")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("--direction <in|out>", 'edge direction: "in" = callers (default), "out" = callees')
     .option("-d, --depth <n>", 'walk transitively up to N hops for blast radius, or "all" for the full connected closure (default 1)')
     .option("--in <path>", "narrow matches to nodes at or under this path prefix")
     .option("--json", "output as JSON")
     .option(...NO_REFRESH_FLAG)
-    .action(async (symbol, dir, opts) => {
+    .action(async (symbol, dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     await refreshBefore(dir, opts);
     const globalOpts = program.opts();
-    if (!opts.json && readWorkspace(resolve(dir), globalOpts.dir)) {
-        runWorkspaceCallers(resolve(dir), globalOpts.dir, symbol, {
+    if (!opts.json && readWorkspace(dir, globalOpts.dir)) {
+        runWorkspaceCallers(dir, globalOpts.dir, symbol, {
             direction: opts.direction === "out" ? "out" : "in",
             depth: opts.depth
                 ? (/^(all|full|max)$/i.test(opts.depth) ? Number.POSITIVE_INFINITY : Number(opts.depth))
@@ -362,17 +388,18 @@ program
     .command("grep")
     .description("Regex search over indexed files, hits grouped by enclosing symbol and ranked by coupling ($0, no LLM)")
     .argument("<pattern>", "regex pattern (or literal string with --fixed)")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("-i, --ignore-case", "case-insensitive match")
     .option("--fixed", "treat pattern as a literal string, not a regex")
     .option("--in <path>", "narrow to files at or under this path prefix")
     .option("--json", "output as JSON")
     .option(...NO_REFRESH_FLAG)
-    .action(async (pattern, dir, opts) => {
+    .action(async (pattern, dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     await refreshBefore(dir, opts);
     const globalOpts = program.opts();
-    if (readWorkspace(resolve(dir), globalOpts.dir)) {
-        runWorkspaceGrep(resolve(dir), globalOpts.dir, pattern, {
+    if (readWorkspace(dir, globalOpts.dir)) {
+        runWorkspaceGrep(dir, globalOpts.dir, pattern, {
             ignoreCase: opts.ignoreCase, fixed: opts.fixed, json: opts.json,
         });
         return;
@@ -389,11 +416,12 @@ program
 program
     .command("map")
     .description("Token-budgeted repo orientation — directory clusters, per-directory hubs, and global hotspots from the wiring graph ($0, no LLM)")
-    .argument("[dir]", "repository root", ".")
+    .argument(...DIR_ARG)
     .option("--max-dirs <n>", "max directory entries shown, rest counted into dropped (default 16)")
     .option("--json", "output as JSON")
     .option(...NO_REFRESH_FLAG)
-    .action(async (dir, opts) => {
+    .action(async (dirArg, opts) => {
+    const dir = queryRoot(dirArg);
     const root = resolve(dir);
     const globalOpts = program.opts();
     let maxDirsW;
@@ -485,8 +513,20 @@ program
         console.error(formatNonInteractiveHelp(detectedIds));
         return;
     }
+    // Workspace parent: every child repo gets its OWN wiring too. A session
+    // opens at a repo root, not at the parent, and reads `.claude/` from there —
+    // wiring only the parent leaves each child with no skill, hooks, or MCP.
+    // The parent's own wiring stays (queries there federate across children).
+    const children = isWorkspaceBuildRoot(repo, program.opts().dir)
+        ? discoverWorkspaceChildren(repo)
+        : [];
+    // Parent FIRST: its build is the workspace build, which builds every child's
+    // graph, so each child's own `buildGraphIfMissing` then finds one and no-ops.
+    const targets = [repo, ...children.map((c) => join(repo, c))];
     if (opts.dryRun) {
         console.error(formatPlan(plan, ids, repo, home));
+        for (const child of children)
+            console.error(`\n— ${child}/ (workspace child)\n` + formatPlan(planInit(join(repo, child), { home }), ids, join(repo, child), home));
         return;
     }
     if (ids.length === 0) {
@@ -495,6 +535,29 @@ program
     }
     const wantClaude = ids.includes("claude");
     const cliPath = fileURLToPath(import.meta.url);
+    if (children.length)
+        console.error(`· workspace: wiring ${repo} and ${children.length} child repo(s) — ${children.join(", ")}`);
+    for (const target of targets) {
+        if (target !== repo)
+            console.error(`\n— ${relative(repo, target)}/`);
+        wireTarget(target, ids, { home, cliPath, plan, opts, wantClaude });
+    }
+    // One epilogue for the whole run. A workspace parent holds no nodes of its
+    // own, so the totals come from the children — the graph the user actually got.
+    const globalDir = program.opts().dir;
+    const graphs = (children.length ? children.map((c) => join(repo, c)) : [repo])
+        .map((d) => loadGraphCached(contextDirFor(d, children.length ? undefined : globalDir)))
+        .filter((g) => g !== null);
+    console.error("\n" +
+        formatInitEpilogue({
+            graphBuilt: graphs.length > 0,
+            nodes: graphs.reduce((n, g) => n + g.meta.nodeCount, 0),
+            edges: graphs.reduce((n, g) => n + g.meta.edgeCount, 0),
+        }));
+});
+/** One repo's worth of `init` writes — the parent, then each workspace child. */
+function wireTarget(repo, ids, ctx) {
+    const { home, cliPath, plan, wantClaude, opts } = ctx;
     if (wantClaude) {
         const res = runInit(repo, { build: opts.build, cliPath });
         console.error(`✓ wrote ${res.settingsPath}`);
@@ -539,16 +602,7 @@ program
             ? "✓ built the graph (graft build)"
             : "· skipped graph build");
     }
-    const globalOpts = program.opts();
-    const outDir = contextDirFor(repo, globalOpts.dir);
-    const graph = loadGraphCached(outDir);
-    console.error("\n" +
-        formatInitEpilogue({
-            graphBuilt: graph !== null,
-            nodes: graph?.meta.nodeCount,
-            edges: graph?.meta.edgeCount,
-        }));
-});
+}
 program.parseAsync().catch((err) => {
     console.error(err instanceof Error ? err.message : err);
     process.exit(1);