@nanonets/graft 0.8.2 → 0.9.1

package/dist/graph/scopes.js

@@ -21,37 +21,26 @@
  *  7. `label` = `prefix` (both "" for root); ordering is prefix-length desc,
  *     then lexicographic.
  */
-import { existsSync, readdirSync, readFileSync, statSync } from "node:fs";
+import { existsSync, readdirSync, readFileSync } from "node:fs";
 import { join, resolve } from "node:path";
-import { SKIP_DIRS } from "../ingest/fs.js";
+import { shouldSkipDir, walkDir } from "../ingest/fs.js";
+import { relPosix } from "../util/paths.js";
+import { readIncludeDirs } from "../util/state.js";
 /** Project-marker files, checked in this order (also the order `markers` is built in). */
 const MARKERS = ["package.json", "go.mod", "pyproject.toml", "setup.py", "Cargo.toml"];
 const CANONICAL_ROOT = [{ prefix: "", label: "", markers: [] }];
-/** Recursively collect every directory under `root` (posix rel path, "" = root itself),
- * reusing `walkDir`'s skip rules (dot-dirs, `SKIP_DIRS`) so build-output and dependency
- * trees are never scanned for markers. */
-function collectDirs(root) {
-    const out = [""];
-    const walk = (absDir, relDir) => {
-        let entries;
-        try {
-            entries = readdirSync(absDir, { withFileTypes: true });
-        }
-        catch {
-            return;
-        }
-        for (const entry of entries) {
-            if (!entry.isDirectory())
-                continue;
-            if (entry.name.startsWith(".") || SKIP_DIRS.has(entry.name))
-                continue;
-            const rel = relDir === "" ? entry.name : `${relDir}/${entry.name}`;
-            out.push(rel);
-            walk(join(absDir, entry.name), rel);
-        }
-    };
-    walk(root, "");
-    return out;
+/** Collect directories represented by the canonical visible file set. Building
+ * this from `walkDir` keeps scope discovery aligned with extraction: an ignored
+ * generated tree cannot become a marker or workspace scope. */
+function collectDirs(root, repoFiles) {
+    const out = new Set([""]);
+    for (const abs of repoFiles) {
+        const parts = relPosix(root, abs).split("/");
+        parts.pop();
+        for (let i = 1; i <= parts.length; i++)
+            out.add(parts.slice(0, i).join("/"));
+    }
+    return [...out];
 }
 /** Minimal `packages:` list parser for `pnpm-workspace.yaml` — no YAML dependency,
  * handles the `packages:\n  - 'glob'\n  - "glob"` form pnpm actually generates. */
@@ -104,10 +93,9 @@ function readWorkspaceGlobs(root) {
     }
     return null;
 }
-/** Resolve one workspace glob to matched dir paths (posix, rel to `root`). Supports
- * only `dir/*` (immediate subdirs) and `dir/**` (any nested depth) forms, implemented
- * with plain `readdir` — no glob dependency, per spec. Unsupported forms resolve empty. */
-function resolveGlob(root, pattern) {
+/** Resolve one workspace glob against visible directories only. Supports
+ * `dir/*` (immediate subdirs), `dir/**` (any nested depth), and literal dirs. */
+function resolveGlob(dirs, pattern) {
     const norm = pattern.replace(/\\/g, "/").replace(/\/$/, "");
     let base;
     let recursive;
@@ -128,57 +116,26 @@ function resolveGlob(root, pattern) {
         recursive = false;
     }
     else if (!norm.includes("*")) {
-        // Literal entry (no glob chars), e.g. `packages: ['apps/*', 'docs']` — a plain
-        // workspace-list entry that names a real directory counts as a workspace match
-        // in its own right, same as a resolved glob would. Without this, a literal
-        // entry silently resolves to nothing while Rule 2 still strips its
-        // `package.json` marker (it's a JS-family dir that never matched the glob
-        // set), de-scoping a real workspace package.
-        try {
-            return existsSync(join(root, norm)) && statSync(join(root, norm)).isDirectory()
-                ? [norm]
-                : [];
-        }
-        catch {
-            return [];
-        }
+        return dirs.includes(norm) ? [norm] : [];
     }
     else {
         return []; // unsupported glob form
     }
-    const results = [];
-    const listDirs = (absDir, relDir) => {
-        let entries;
-        try {
-            entries = readdirSync(absDir, { withFileTypes: true });
-        }
-        catch {
-            return [];
-        }
-        return entries
-            .filter((e) => e.isDirectory() && !e.name.startsWith(".") && !SKIP_DIRS.has(e.name))
-            .map((e) => (relDir === "" ? e.name : `${relDir}/${e.name}`));
-    };
-    const baseAbs = base === "" ? root : join(root, base);
-    if (!recursive) {
-        results.push(...listDirs(baseAbs, base));
-    }
-    else {
-        const stack = [base];
-        while (stack.length) {
-            const relDir = stack.pop();
-            const absDir = relDir === "" ? root : join(root, relDir);
-            const children = listDirs(absDir, relDir);
-            results.push(...children);
-            stack.push(...children);
-        }
-    }
-    return results;
+    return dirs.filter((dir) => {
+        if (dir === "")
+            return false;
+        if (recursive)
+            return base === "" || dir.startsWith(`${base}/`);
+        const slash = dir.lastIndexOf("/");
+        const parent = slash === -1 ? "" : dir.slice(0, slash);
+        return parent === base;
+    });
 }
-/** Walk the tree (reusing `walkDir`'s skip rules) and find project-marker dirs. */
-export function discoverScopes(root) {
+/** Walk the tree (reusing `walkDir`'s skip rules, including the repo's persisted
+ * `--include-dir` override) and find project-marker dirs. */
+export function discoverScopes(root, repoFiles = walkDir(root, readIncludeDirs(resolve(root)))) {
     const absRoot = resolve(root);
-    const dirs = collectDirs(absRoot);
+    const dirs = collectDirs(absRoot, repoFiles);
     const markerMap = new Map();
     for (const dir of dirs) {
         const found = MARKERS.filter((m) => existsSync(join(absRoot, dir, m)));
@@ -189,7 +146,7 @@ export function discoverScopes(root) {
     const workspaceMatches = new Set();
     if (workspaceGlobs) {
         for (const glob of workspaceGlobs) {
-            for (const dir of resolveGlob(absRoot, glob))
+            for (const dir of resolveGlob(dirs, glob))
                 workspaceMatches.add(dir);
         }
     }
@@ -342,10 +299,26 @@ export function scopesHereClause(scopes) {
 export function pathUnderPrefix(path, prefix) {
     return prefix === "" || path === prefix || path.startsWith(`${prefix}/`);
 }
+/**
+ * Validate a normalized `--in` prefix against the graph before a query runs. A
+ * prefix matching no indexed node is a caller mistake (typo, wrong sub-project,
+ * or a mid-path fragment where a prefix is required) rather than a legitimate
+ * zero-hit query, so every `--in`-taking command fails loudly and identically
+ * instead of printing empty output the caller has to interpret.
+ *
+ * Pass the prefix through `normalizePathPrefix` first — an un-normalized
+ * `src\gpu` or `src/` will not match anything here.
+ */
+export function assertPrefixIndexed(graph, prefix) {
+    if (!prefix || graph.nodes.some((n) => pathUnderPrefix(n.path, prefix)))
+        return;
+    throw new Error(`nothing indexed under "${prefix}/"${scopesHereClause(scopesOfGraph(graph))} (or any path prefix)`);
+}
 /** Immediate subdirs of `root` that are themselves git repos (have `.git`).
  * Used by workspace federation (Task 5). */
 export function discoverWorkspaceChildren(root) {
     const absRoot = resolve(root);
+    const includes = readIncludeDirs(absRoot);
     let entries;
     try {
         entries = readdirSync(absRoot, { withFileTypes: true });
@@ -354,10 +327,7 @@ export function discoverWorkspaceChildren(root) {
         return [];
     }
     return entries
-        .filter((e) => e.isDirectory() &&
-        !e.name.startsWith(".") &&
-        !SKIP_DIRS.has(e.name) &&
-        existsSync(join(absRoot, e.name, ".git")))
+        .filter((e) => e.isDirectory() && !shouldSkipDir(e.name, includes) && existsSync(join(absRoot, e.name, ".git")))
         .map((e) => e.name);
 }
 /** Every consumer's entry point to a graph's scopes: absent `meta.scopes` (old

package/dist/graph/scopes.js.map

@@ -1 +1 @@
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package/dist/graph/seed.d.ts

@@ -0,0 +1,38 @@
+/** Env kill switch, mirroring `GRAFT_NO_REFRESH` in ./refresh.ts. */
+export declare function seedDisabled(): boolean;
+/**
+ * The main checkout of the repo `root` is a linked worktree of, or null when `root`
+ * isn't one (which is the common case, and not an error).
+ *
+ * Filesystem-only on purpose: no `git` subprocess on a path that runs before every
+ * query. The shapes it has to tell apart:
+ *
+ * - `<root>/.git` is a **directory** → this *is* the main checkout. Nothing to seed.
+ * - `gitdir: <main>/.git/worktrees/<name>` → a linked worktree. `commondir` inside
+ *   that dir points back at the shared `.git` (`../..`), whose parent is the main
+ *   checkout.
+ * - `gitdir: <super>/.git/modules/<name>` → a **submodule**. Identical file shape,
+ *   completely different thing: a submodule is its own repo and its parent's `graft/`
+ *   describes different code entirely. The `worktrees` path segment is what rejects it.
+ * - A bare repo or `--separate-git-dir` layout, where the resolved common dir isn't
+ *   named `.git` and there may be no working tree at all → null.
+ */
+export declare function mainWorktreeRoot(root: string): string | null;
+export interface SeedResult {
+    seeded: boolean;
+    /** The main checkout the graph came from, when one was used. */
+    from?: string;
+}
+/**
+ * Copy the parent checkout's graph into `root`'s own `graft/`, if all of this holds:
+ * `root` is a linked worktree, it has no graph yet, the parent has one, and no `--dir`
+ * override is in play (a custom output dir can't be mapped to a sibling checkout —
+ * the same conservatism `ensureGitignored` applies).
+ *
+ * Best-effort by contract: the caller's fallback is the behaviour that existed before
+ * this function did, so every failure returns `{ seeded: false }` rather than raising.
+ */
+export declare function seedGraph(root: string, opts?: {
+    contextDir?: string;
+}): SeedResult;
+//# sourceMappingURL=seed.d.ts.map

package/dist/graph/seed.d.ts.map

@@ -0,0 +1 @@
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package/dist/graph/seed.js

@@ -0,0 +1,226 @@
+/**
+ * `seedGraph` — give a linked git worktree the graph its parent checkout already has.
+ *
+ * `graft/` is a local cache, so it is gitignored, so `git worktree add` never checks
+ * it out: a worktree starts with `src/` and `.claude/` and no graph at all. Every
+ * MCP tool then answers "no graph found — run graft build first" for the whole
+ * session, and the passive surface (`INDEX.md`, the cards) is missing too. The agent
+ * that was supposed to be cheapest in a fresh worktree is instead blind in one.
+ *
+ * What travels is the graph and the sidecars a query reads — never the markdown; see
+ * `seedable` for why the cards are the parent's branch and not this one's.
+ *
+ * The parent checkout has not gone anywhere, though — a worktree's `.git` is a *file*
+ * naming it, and the harness that creates these worktrees already reaches back the
+ * same way (Claude Code symlinks `node_modules` to the parent's). So: copy the
+ * parent's `graft/` in, then let the ordinary refresh gate repair the difference.
+ *
+ * Copy, not symlink. `node_modules` is the same for every branch; a graph is a set of
+ * `file:line` spans for one specific tree, so a shared one would have the worktree
+ * rewriting the parent's graph with its own branch's line numbers. What makes the
+ * copy worth doing rather than just rebuilding cold:
+ *
+ * - **The Tier-2 meaning layer survives.** Summaries and cruxes cost real money;
+ *   `buildGraph` folds a prior `wiring.json` in by `body_hash`, so an unchanged
+ *   function keeps the summary someone already paid for. A cold build throws them all
+ *   away and the worktree silently drops to structural-only answers.
+ * - **The repair is small.** `probeDrift` confirms a suspect file by content hash, so
+ *   a fresh checkout's brand-new mtimes cost one hashing pass and nothing more; the
+ *   drift that survives is exactly the diff between the two checkouts' commits.
+ * - **$0 and offline**, like everything else on the query path.
+ *
+ * Never writes to the parent, never throws, and no-ops unless there is genuinely a
+ * built parent checkout on disk — so a fresh clone, CI, or a cloud session whose repo
+ * was *cloned* rather than worktree'd behaves exactly as it did before: "run graft
+ * build first".
+ */
+import { copyFileSync, existsSync, mkdirSync, readFileSync, readdirSync, renameSync, rmSync, statSync, } from "node:fs";
+import { basename, dirname, isAbsolute, join, resolve } from "node:path";
+import { ASK_INDEX_FILE } from "../ask/index-file.js";
+import { CACHE_DIR, contextDirFor } from "../context/node-file.js";
+import { EXTRACT_CACHE_PREFIX } from "./extract-cache.js";
+import { FINGERPRINT_PREFIX } from "./fingerprint.js";
+import { GRAPH_DIR, wiringPath } from "./write.js";
+/** The one line a linked worktree's `.git` file carries. */
+const GITDIR_KEY = "gitdir:";
+/** Env kill switch, mirroring `GRAFT_NO_REFRESH` in ./refresh.ts. */
+export function seedDisabled() {
+    const v = process.env.GRAFT_NO_SEED;
+    return v !== undefined && v !== "" && v !== "0" && v !== "false";
+}
+/**
+ * The main checkout of the repo `root` is a linked worktree of, or null when `root`
+ * isn't one (which is the common case, and not an error).
+ *
+ * Filesystem-only on purpose: no `git` subprocess on a path that runs before every
+ * query. The shapes it has to tell apart:
+ *
+ * - `<root>/.git` is a **directory** → this *is* the main checkout. Nothing to seed.
+ * - `gitdir: <main>/.git/worktrees/<name>` → a linked worktree. `commondir` inside
+ *   that dir points back at the shared `.git` (`../..`), whose parent is the main
+ *   checkout.
+ * - `gitdir: <super>/.git/modules/<name>` → a **submodule**. Identical file shape,
+ *   completely different thing: a submodule is its own repo and its parent's `graft/`
+ *   describes different code entirely. The `worktrees` path segment is what rejects it.
+ * - A bare repo or `--separate-git-dir` layout, where the resolved common dir isn't
+ *   named `.git` and there may be no working tree at all → null.
+ */
+export function mainWorktreeRoot(root) {
+    try {
+        const dot = join(root, ".git");
+        if (statSync(dot).isDirectory())
+            return null;
+        // Read the pointer without a regex. `/^gitdir:[ \t]*(.+?)[ \t]*$/m` is the
+        // polynomial-ReDoS shape CodeQL flagged on `ensureSearchable` (`js/polynomial-redos`,
+        // fixed in 44a191e): `.` also matches space and tab, so the lazy group and the
+        // trailing `[ \t]*` overlap and a line of blanks costs O(n²). Same conclusion as
+        // that fix — the ambiguity buys nothing, and split/startsWith/trim is linear and
+        // plainer. `trim` also absorbs the `\r` of a CRLF checkout.
+        const line = readFileSync(dot, "utf8").split("\n").find((l) => l.startsWith(GITDIR_KEY));
+        if (line === undefined)
+            return null;
+        const target = line.slice(GITDIR_KEY.length).trim();
+        if (!target)
+            return null;
+        const gitdir = isAbsolute(target) ? target : resolve(root, target);
+        if (basename(dirname(gitdir)) !== "worktrees")
+            return null;
+        const rel = readFileSync(join(gitdir, "commondir"), "utf8").trim();
+        if (!rel)
+            return null;
+        const common = isAbsolute(rel) ? rel : resolve(gitdir, rel);
+        if (basename(common) !== ".git" || !statSync(common).isDirectory())
+            return null;
+        const main = dirname(common);
+        if (resolve(main) === resolve(root))
+            return null;
+        return main;
+    }
+    catch {
+        // No `.git` at all, an unreadable one, a `commondir` that doesn't exist: all of
+        // them mean "can't seed from here", which is the same answer as "not a worktree".
+        return null;
+    }
+}
+const NOT_SEEDED = { seeded: false };
+/**
+ * An allowlist, not a skip list: is this repo-relative path (posix) one of the few
+ * files a seed may bring across?
+ *
+ * The gate that calls this promises "writes only what a query reads — the graph, the
+ * `ask` sidecar, the freshness record" (see the header of ./refresh.ts). A copy that
+ * wrote anything else would turn a read into a write of the repo, so the copy honours
+ * the same list. The extraction memo is on it because the refresh immediately after
+ * rewrites that file anyway, and replaying it is what keeps the repair cheap.
+ *
+ * **Deliberately absent: the cards and `INDEX.md`.** They would land as this
+ * checkout's documentation while describing the *parent's* branch, and nothing on the
+ * query path rewrites them (`writeCards`/`writeIndex` sit behind `!graphOnly`), so they
+ * would stay wrong indefinitely. An explicit `graft build` regenerates them from this
+ * checkout's own graph — and prunes the ones that no longer apply — which is both
+ * correct and nearly free once the graph is here.
+ *
+ * Also absent, because it belongs to the checkout that produced it: `.cache/session/`
+ * (another session's transcripts), `.sync.lock` (another process's lock), and
+ * `stats.json` (this checkout earns its own savings and dirty flag).
+ */
+function seedable(rel) {
+    // The dirs themselves, or cpSync would never look inside them.
+    if (rel === "" || rel === GRAPH_DIR || rel === CACHE_DIR)
+        return true;
+    if (!rel.startsWith(`${CACHE_DIR}/`))
+        return false; // incl. the graph: `installGraph` places it
+    const name = rel.slice(CACHE_DIR.length + 1);
+    return (name === ASK_INDEX_FILE ||
+        name.startsWith(`${EXTRACT_CACHE_PREFIX}.`) ||
+        name.startsWith(`${FINGERPRINT_PREFIX}.`));
+}
+/**
+ * Copy `srcDir` into `outDir`, keeping only what {@link seedable} allows.
+ *
+ * Walked by hand rather than through `cpSync`'s `filter`, which did not hold on
+ * Windows: the graph arrived — it is placed directly, by {@link installGraph} — while
+ * every allowlisted sidecar next to it was dropped. A seeded worktree therefore had no
+ * fingerprint, `probeDrift` read that as "never built", and the query right behind the
+ * seed rebuilt the whole repo instead of the diff against the parent: precisely the
+ * cost seeding exists to avoid, and silent, because a full rebuild still answers
+ * correctly. It only surfaced as a `(? files changed)` note on the CI leg.
+ *
+ * Composing `rel` from the segments this walk joined itself is what fixes it — the
+ * allowlist no longer depends on the form `cpSync` chooses to hand its callback, and
+ * `rel` is posix by construction rather than by conversion. Also narrower than the old
+ * copy in one way worth keeping: only real files and directories travel, never a
+ * symlink, and nothing in the allowlist is one.
+ */
+function copyTree(srcDir, outDir) {
+    const walk = (rel) => {
+        const from = rel ? join(srcDir, rel) : srcDir;
+        mkdirSync(rel ? join(outDir, rel) : outDir, { recursive: true });
+        for (const entry of readdirSync(from, { withFileTypes: true })) {
+            const childRel = rel ? `${rel}/${entry.name}` : entry.name;
+            if (!seedable(childRel))
+                continue;
+            if (entry.isDirectory())
+                walk(childRel);
+            else if (entry.isFile())
+                copyFileSync(join(from, entry.name), join(outDir, childRel));
+        }
+    };
+    walk("");
+}
+/**
+ * Put `wiring.json` in place last, via a temp file and a rename.
+ *
+ * Its presence is the flag every caller reads to mean "this repo has a graph"
+ * (`refresh.ts`, `workspace.ts`, every MCP tool). So it must appear only once the
+ * rest of the copy has landed and must never appear half-written: a seed killed
+ * midway then leaves no graph, and the next call simply seeds again.
+ */
+function installGraph(srcGraph, destGraph) {
+    mkdirSync(dirname(destGraph), { recursive: true });
+    const tmp = `${destGraph}.seed.${process.pid}`;
+    try {
+        copyFileSync(srcGraph, tmp);
+        renameSync(tmp, destGraph);
+    }
+    catch (err) {
+        try {
+            rmSync(tmp, { force: true });
+        }
+        catch { /* nothing to clean up */ }
+        throw err;
+    }
+}
+/**
+ * Copy the parent checkout's graph into `root`'s own `graft/`, if all of this holds:
+ * `root` is a linked worktree, it has no graph yet, the parent has one, and no `--dir`
+ * override is in play (a custom output dir can't be mapped to a sibling checkout —
+ * the same conservatism `ensureGitignored` applies).
+ *
+ * Best-effort by contract: the caller's fallback is the behaviour that existed before
+ * this function did, so every failure returns `{ seeded: false }` rather than raising.
+ */
+export function seedGraph(root, opts = {}) {
+    if (opts.contextDir || seedDisabled())
+        return NOT_SEEDED;
+    try {
+        const dir = resolve(root);
+        const outDir = contextDirFor(dir);
+        if (existsSync(wiringPath(outDir)))
+            return NOT_SEEDED; // already has its own
+        const main = mainWorktreeRoot(dir);
+        if (!main)
+            return NOT_SEEDED;
+        const srcDir = contextDirFor(main);
+        const srcGraph = wiringPath(srcDir);
+        if (!existsSync(srcGraph))
+            return NOT_SEEDED; // parent never built either
+        copyTree(srcDir, outDir);
+        installGraph(srcGraph, wiringPath(outDir));
+        return { seeded: true, from: main };
+    }
+    catch {
+        return NOT_SEEDED;
+    }
+}
+//# sourceMappingURL=seed.js.map

package/dist/graph/seed.js.map

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package/dist/graph/source-files.d.ts

@@ -1,10 +1,18 @@
-/** The source files a graph build parses: supported languages, minus the output dir. */
-export declare function listSourceFiles(root: string, outDir: string): string[];
+/**
+ * The source files a graph build parses: supported languages, minus the
+ * output dir. When no pre-enumerated `repoFiles` is passed, the walk reads
+ * `root`'s persisted `--include-dir` override (if any) directly from state —
+ * so every caller that enumerates through here (the fingerprint probe, the
+ * hooks/refresh path, none of which ever see a CLI flag) behaves identically
+ * to the `graft build --include-dir` invocation that set it.
+ */
+export declare function listSourceFiles(root: string, outDir: string, repoFiles?: string[]): string[];
 export interface SourceStat {
     /** Absolute path. */
     abs: string;
-    /** `relative(root, abs)` — exactly the form `buildGraph` uses for node ids and
-     * `checkGraph` diffs against, so cache keys and ids can never disagree. */
+    /** Repo-relative, posix (`relPosix`) — exactly the form `buildGraph` uses for
+     * node ids and `checkGraph` diffs against, so cache keys and ids can never
+     * disagree. Posix on every platform: see `../util/paths.ts`. */
     rel: string;
     size: number;
     mtimeMs: number;
@@ -14,5 +22,5 @@ export interface SourceStat {
  * both the freshness probe and the extraction cache. Files that vanish between
  * the walk and the stat are dropped (same fail-soft posture as `walkDir`).
  */
-export declare function listSourceStats(root: string, outDir: string): SourceStat[];
+export declare function listSourceStats(root: string, outDir: string, repoFiles?: string[]): SourceStat[];
 //# sourceMappingURL=source-files.d.ts.map

package/dist/graph/source-files.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"source-files.d.ts","sourceRoot":"","sources":["../../src/graph/source-files.ts"],"names":[],"mappings":"AAeA;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,GAAE,MAAM,EAAkD,GAClE,MAAM,EAAE,CAEV;AAED,MAAM,WAAW,UAAU;IACzB,qBAAqB;IACrB,GAAG,EAAE,MAAM,CAAC;IACZ;;oEAEgE;IAChE,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,EAAE,GAAG,UAAU,EAAE,CAYhG"}

package/dist/graph/source-files.js

@@ -7,21 +7,30 @@
  * {@link listSourceFiles} so its existing importers are unaffected.
  */
 import { statSync } from "node:fs";
-import { relative } from "node:path";
+import { resolve } from "node:path";
 import { walkDir } from "../ingest/fs.js";
+import { relPosix } from "../util/paths.js";
+import { readIncludeDirs } from "../util/state.js";
 import { languageOf } from "./extract.js";
-/** The source files a graph build parses: supported languages, minus the output dir. */
-export function listSourceFiles(root, outDir) {
-    return walkDir(root).filter((f) => !f.startsWith(outDir) && languageOf(f) !== null);
+/**
+ * The source files a graph build parses: supported languages, minus the
+ * output dir. When no pre-enumerated `repoFiles` is passed, the walk reads
+ * `root`'s persisted `--include-dir` override (if any) directly from state —
+ * so every caller that enumerates through here (the fingerprint probe, the
+ * hooks/refresh path, none of which ever see a CLI flag) behaves identically
+ * to the `graft build --include-dir` invocation that set it.
+ */
+export function listSourceFiles(root, outDir, repoFiles = walkDir(root, readIncludeDirs(resolve(root)))) {
+    return repoFiles.filter((f) => !f.startsWith(outDir) && languageOf(f) !== null);
 }
 /**
  * {@link listSourceFiles} plus each file's `(size, mtimeMs)` — the currency of
  * both the freshness probe and the extraction cache. Files that vanish between
  * the walk and the stat are dropped (same fail-soft posture as `walkDir`).
  */
-export function listSourceStats(root, outDir) {
+export function listSourceStats(root, outDir, repoFiles) {
     const out = [];
-    for (const abs of listSourceFiles(root, outDir)) {
+    for (const abs of listSourceFiles(root, outDir, repoFiles)) {
         let s;
         try {
             s = statSync(abs);
@@ -29,7 +38,7 @@ export function listSourceStats(root, outDir) {
         catch {
             continue;
         }
-        out.push({ abs, rel: relative(root, abs), size: s.size, mtimeMs: s.mtimeMs });
+        out.push({ abs, rel: relPosix(root, abs), size: s.size, mtimeMs: s.mtimeMs });
     }
     return out;
 }

package/dist/graph/source-files.js.map

@@ -1 +1 @@
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+{"version":3,"file":"source-files.js","sourceRoot":"","sources":["../../src/graph/source-files.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AACH,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AACnC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACnD,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAE1C;;;;;;;GAOG;AACH,MAAM,UAAU,eAAe,CAC7B,IAAY,EACZ,MAAc,EACd,YAAsB,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC;IAEnE,OAAO,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,CAAC,IAAI,UAAU,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAClF,CAAC;AAaD;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAAC,IAAY,EAAE,MAAc,EAAE,SAAoB;IAChF,MAAM,GAAG,GAAiB,EAAE,CAAC;IAC7B,KAAK,MAAM,GAAG,IAAI,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,CAAC;QAC3D,IAAI,CAAoC,CAAC;QACzC,IAAI,CAAC;YACH,CAAC,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;QACpB,CAAC;QAAC,MAAM,CAAC;YACP,SAAS;QACX,CAAC;QACD,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,EAAE,QAAQ,CAAC,IAAI,EAAE,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;IAChF,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/graph/traverse-cli.d.ts

@@ -26,8 +26,14 @@ export declare function callersSavings(graph: GraphV1, results: {
     symbol: NodeV1;
     hits: EdgeHit[];
 }[]): Savings | undefined;
-/** Loud, actionable empty-result note — never a bare empty list. */
-export declare function looseNoteFor(direction: Direction, name: string): string;
+/** Loud, actionable empty-result note — never a bare empty list. `candidateCount`
+ * is how many nodes {@link resolveSymbol} matched for this query (both call
+ * sites already hold it as `matches.length`) — when it's >1, the query name is
+ * itself ambiguous (several definitions share it), which is exactly the case
+ * `resolve.ts` drops a cross-file call/reference for rather than guessing which
+ * one it means. Without saying so, a zero-hit result here reads as "nothing
+ * calls this" when it may really be "something does, but the edge was dropped". */
+export declare function looseNoteFor(direction: Direction, name: string, candidateCount: number): string;
 /**
  * Resolve `query` in the graph at `dir` (respecting `--dir`/`--in`), walk edges
  * per `--direction`/`--depth`, and print either the human report or `--json`.

package/dist/graph/traverse-cli.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"traverse-cli.d.ts","sourceRoot":"","sources":["../../src/graph/traverse-cli.ts"],"names":[],"mappings":"AAeA,OAAO,EAA2B,KAAK,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAE9E,OAAO,EAA2B,KAAK,SAAS,EAAE,KAAK,OAAO,EAAE,MAAM,eAAe,CAAC;AACtF,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAC;AAElD,MAAM,WAAW,iBAAiB;IAChC,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,uEAAuE;IACvE,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,gFAAgF;IAChF,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,oFAAoF;IACpF,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAKD;;kFAEkF;AAClF,wBAAgB,QAAQ,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE1C;AAED;sEACsE;AACtE,wBAAgB,OAAO,CAAC,SAAS,EAAE,SAAS,EAAE,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,OAAO,GAAG,MAAM,CAKtF;AAED;;;sCAGsC;AACtC,wBAAgB,cAAc,CAC5B,KAAK,EAAE,OAAO,EACd,OAAO,EAAE;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,OAAO,EAAE,CAAA;CAAE,EAAE,GAC7C,OAAO,GAAG,SAAS,CAOrB;AAED;;;;;;mFAMmF;AACnF,wBAAgB,YAAY,CAAC,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,GAAG,MAAM,CAQ/F;AAiDD;;;;;GAKG;AACH,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,iBAAiB,GAAG,IAAI,CA0E3F"}