@nanonets/graft 0.18.0 → 0.20.0

package/dist/app/server.js

@@ -20,7 +20,8 @@ import { createServer } from "node:http";
 import { timingSafeEqual } from "node:crypto";
 import { jobKey, reviewJobFor } from "./events.js";
 import { InstallationTokens, verifySignature } from "./identity.js";
-import { buildRepoIntoBrain, RepoNotAccessibleError } from "./brain-build.js";
+import { checkRepoAccess, RepoNotAccessibleError } from "./brain-build.js";
+import { buildRepoInChildProcess } from "./brain-build-process.js";
 import { PageStore } from "./pages.js";
 import { WorkQueue } from "./queue.js";
 import { reviewInChildProcess } from "./review-process.js";
@@ -96,6 +97,51 @@ export function createApp(config, seams = {}) {
             log(`${jobKey(decided.job)}: queued${decided.job.fromFork ? " (fork)" : ""}`);
             return send(res, 202, "application/json", JSON.stringify({ queued: true }));
         }
+        // Can we read this repository? The cheap question, answered on its own.
+        //
+        // Same secret as /brain/build, because it is the same caller and the same
+        // trust. Kept separate from it because it costs a second where the build
+        // costs minutes, and the platform needs the answer before it can decide
+        // which screen to show.
+        if (req.method === "POST" && url.pathname === "/brain/access") {
+            if (!config.brainBuildSecret)
+                return send(res, 404, "text/plain", "not found");
+            if (!bearerMatches(header(req, "authorization"), config.brainBuildSecret)) {
+                return send(res, 401, "text/plain", "unauthorized");
+            }
+            const body = await readBody(req);
+            if (body === null)
+                return send(res, 413, "text/plain", "payload too large");
+            let ask;
+            try {
+                ask = JSON.parse(body);
+            }
+            catch {
+                return send(res, 400, "text/plain", "bad json");
+            }
+            if (!ask.owner || !ask.repo) {
+                return send(res, 400, "application/json", JSON.stringify({ error: "owner and repo are required" }));
+            }
+            try {
+                const access = await (seams.brainAccess ?? checkRepoAccess)({ owner: ask.owner, repo: ask.repo }, {
+                    creds: config,
+                    fetch: fetchImpl,
+                    api: config.api,
+                    publicToken: config.publicToken,
+                    publicOwner: config.publicOwner,
+                    log,
+                    now: seams.now,
+                });
+                // 200 either way: "we cannot see it" is an answer, not a failure, and
+                // the platform turns it into a choice rather than an error.
+                return send(res, 200, "application/json", JSON.stringify(access));
+            }
+            catch (e) {
+                const msg = e instanceof Error ? e.message : String(e);
+                log(`brain access ${ask.owner}/${ask.repo} failed: ${msg}`);
+                return send(res, 502, "application/json", JSON.stringify({ error: msg }));
+            }
+        }
         // Build one repository into a brain, on demand. Called by the platform when
         // someone pastes a repository URL during onboarding — there is no webhook
         // behind it, so it authenticates with a bearer token rather than a payload
@@ -132,10 +178,17 @@ export function createApp(config, seams = {}) {
                 // request cannot redirect a repository's history to another host.
                 if (config.brainBaseUrl)
                     job.brainBaseUrl = config.brainBaseUrl;
-                const built = await (seams.brainBuild ?? buildRepoIntoBrain)(job, {
+                // Out of this process by default. A read is minutes of blocking work
+                // and the App has to keep answering — including the one-second access
+                // question the next person's onboarding is waiting on. A test that
+                // injects its own builder still runs in-process, which is what a test
+                // wants.
+                const built = await (seams.brainBuild ?? buildRepoInChildProcess)(job, {
                     creds: config,
                     fetch: fetchImpl,
                     api: config.api,
+                    publicToken: config.publicToken,
+                    publicOwner: config.publicOwner,
                     log,
                     now: seams.now,
                 });

package/dist/app/server.js.map

@@ -1 +1 @@
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package/dist/app/sources.d.ts

@@ -1,4 +1,4 @@
-import type { Fetch } from "./identity.js";
+import { type Fetch } from "./identity.js";
 /** What kind of thing a source is, so extraction can weigh it. */
 export type SourceKind = "agent_instructions" | "decision_doc" | "lint_config" | "ci_config" | "codeowners" | "branch_protection" | "revert" | "test_name" | "declined_issue";
 /** One rule-bearing artefact. */

package/dist/app/sources.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sources.d.ts","sourceRoot":"","sources":["../../src/app/sources.ts"],"names":[],"mappings":"AAeA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,eAAe,CAAC;AAE3C,kEAAkE;AAClE,MAAM,MAAM,UAAU,GAClB,oBAAoB,GACpB,cAAc,GACd,aAAa,GACb,WAAW,GACX,YAAY,GACZ,mBAAmB,GACnB,QAAQ,GACR,WAAW,GACX,gBAAgB,CAAC;AAErB,iCAAiC;AACjC,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,UAAU,CAAC;IACjB,8EAA8E;IAC9E,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,iEAAiE;IACjE,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAkCD;;;;;;;;;GASG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CAenE;AASD,sEAAsE;AACtE,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CAiB9D;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CA0B/D;AAED,kEAAkE;AAClE,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CAM5D;AAiBD;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,SAAc,GAAG,aAAa,EAAE,CAe5E;AAKD;;;;;;;;;GASG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,EAAE,GAAG,SAAiB,GAAG,aAAa,EAAE,CAUvH;AAqBD;;;;;;GAMG;AACH,wBAAsB,kBAAkB,CACtC,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,KAAK,EAChB,GAAG,SAA2B,EAC9B,GAAG,SAAe,GACjB,OAAO,CAAC,aAAa,EAAE,CAAC,CAkC1B;AAED,2DAA2D;AAC3D,wBAAsB,oBAAoB,CACxC,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,KAAK,EAChB,GAAG,SAA2B,GAC7B,OAAO,CAAC,aAAa,EAAE,CAAC,CA2B1B;AAsBD,wBAAgB,aAAa,CAAC,OAAO,EAAE,aAAa,EAAE,EAAE,QAAQ,SAAkB,EAAE,QAAQ,SAAc,GAAG,aAAa,EAAE,CAW3H;AAED,8DAA8D;AAC9D,wBAAgB,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,CAEzD"}
+{"version":3,"file":"sources.d.ts","sourceRoot":"","sources":["../../src/app/sources.ts"],"names":[],"mappings":"AAeA,OAAO,EAAa,KAAK,KAAK,EAAE,MAAM,eAAe,CAAC;AAEtD,kEAAkE;AAClE,MAAM,MAAM,UAAU,GAClB,oBAAoB,GACpB,cAAc,GACd,aAAa,GACb,WAAW,GACX,YAAY,GACZ,mBAAmB,GACnB,QAAQ,GACR,WAAW,GACX,gBAAgB,CAAC;AAErB,iCAAiC;AACjC,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,UAAU,CAAC;IACjB,8EAA8E;IAC9E,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,iEAAiE;IACjE,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAkCD;;;;;;;;;GASG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CAenE;AASD,sEAAsE;AACtE,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CAiB9D;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CA0B/D;AAED,kEAAkE;AAClE,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,EAAE,CAM5D;AAiBD;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,SAAc,GAAG,aAAa,EAAE,CAe5E;AAKD;;;;;;;;;GASG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,EAAE,GAAG,SAAiB,GAAG,aAAa,EAAE,CAUvH;AAqBD;;;;;;GAMG;AACH,wBAAsB,kBAAkB,CACtC,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,KAAK,EAChB,GAAG,SAA2B,EAC9B,GAAG,SAAe,GACjB,OAAO,CAAC,aAAa,EAAE,CAAC,CAkC1B;AAED,2DAA2D;AAC3D,wBAAsB,oBAAoB,CACxC,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,KAAK,EAChB,GAAG,SAA2B,GAC7B,OAAO,CAAC,aAAa,EAAE,CAAC,CA2B1B;AAsBD,wBAAgB,aAAa,CAAC,OAAO,EAAE,aAAa,EAAE,EAAE,QAAQ,SAAkB,EAAE,QAAQ,SAAc,GAAG,aAAa,EAAE,CAW3H;AAED,8DAA8D;AAC9D,wBAAgB,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,CAEzD"}

package/dist/app/sources.js

@@ -13,6 +13,7 @@
 import { readFileSync, existsSync, readdirSync, statSync } from "node:fs";
 import { join, relative } from "node:path";
 import { spawnSync } from "node:child_process";
+import { ghHeaders } from "./identity.js";
 /** Per-file and total caps, so one enormous doc cannot crowd out everything. */
 const MAX_FILE_CHARS = 24_000;
 const MAX_TOTAL_CHARS = 300_000;
@@ -237,7 +238,7 @@ const MAX_DECLINED = 40;
 export async function readDeclinedIssues(owner, repo, token, fetchImpl, api = "https://api.github.com", max = MAX_DECLINED) {
     try {
         const res = await fetchImpl(`${api}/repos/${owner}/${repo}/issues?state=closed&per_page=100&sort=updated`, {
-            headers: { authorization: `Bearer ${token}`, accept: "application/vnd.github+json", "user-agent": "graft-app" },
+            headers: ghHeaders(token),
         });
         if (!res.ok)
             return [];
@@ -275,7 +276,7 @@ export async function readBranchProtection(owner, repo, branch, token, fetchImpl
         return [];
     try {
         const res = await fetchImpl(`${api}/repos/${owner}/${repo}/branches/${encodeURIComponent(branch)}/protection`, {
-            headers: { authorization: `Bearer ${token}`, accept: "application/vnd.github+json", "user-agent": "graft-app" },
+            headers: ghHeaders(token),
         });
         // 404 simply means the branch is not protected, which is not a failure.
         if (!res.ok)

package/dist/app/sources.js.map

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package/dist/ask/ask.js

@@ -1094,7 +1094,7 @@ export function ask(dir, query, opts = {}) {
         result.saved = baselineFor(result.hits, corpus.graph);
         // What the team decided about the code this pack just inlined. Read from the
         // local cache only — `ask` is on the agent's hot path and must never wait on
-        // the network; `graft brain pull` and `init` are what refresh it.
+        // the network; `graft trail pull` and `init` are what refresh it.
         const applied = attachBrainRules(root, result.hits, corpus.graph);
         if (applied.length)
             result.rules = applied;

package/dist/brain/claude-md.d.ts

@@ -0,0 +1,59 @@
+/**
+ * `graft claude-md pull`: write the CLAUDE.md changes accepted in Trail into
+ * this checkout's instruction file.
+ *
+ * Trail compares the repository's CLAUDE.md with what its history says and
+ * suggests edits and new sections; a person accepts some of them on the brain's
+ * CLAUDE.md page. This fetches the accepted ones, applies them to the local
+ * file, and tells Trail which it wrote so the page stops listing them.
+ *
+ * The file is edited line by line, never regenerated, so everything a change
+ * does not touch comes back byte for byte. An edit whose text is no longer in
+ * its section means the local file has moved on since Trail read it; that
+ * change is reported and left, never guessed at. Same rules as Trail's own
+ * ComposeClaudeMd, which is what the page's preview shows.
+ */
+import { type BrainLink } from "./link.js";
+/** One accepted change, as Trail sends it. */
+export interface ClaudeMdChange {
+    id: string;
+    kind: "edit" | "add";
+    /** edit: the section it rewrites. add: the new section's heading. */
+    heading: string;
+    /** add: the section it goes after; "" = end of file. */
+    after_heading?: string;
+    /** edit: the text to replace; "" = append to the section. */
+    find?: string;
+    text: string;
+    reason?: string;
+}
+export interface ClaudeMdPull {
+    /** The file Trail read, e.g. "CLAUDE.md"; "" when the repo had none. */
+    path: string;
+    head_sha: string;
+    changes: ClaudeMdChange[];
+}
+export interface ApplyResult {
+    text: string;
+    /** Written by this pull. */
+    written: ClaudeMdChange[];
+    /** Already in the file (committed by someone else): nothing to write. */
+    present: ClaudeMdChange[];
+    /** Could not be placed; the file was left as it is for these. */
+    skipped: Array<{
+        change: ClaudeMdChange;
+        why: string;
+    }>;
+}
+/** GET /api/public/brains/:id/claude-md — the accepted changes. */
+export declare function fetchAcceptedChanges(link: BrainLink, fetchImpl?: typeof fetch): Promise<ClaudeMdPull | {
+    error: string;
+}>;
+/** POST /api/public/brains/:id/claude-md/applied — what this pull wrote. */
+export declare function markApplied(link: BrainLink, ids: string[], fetchImpl?: typeof fetch): Promise<boolean>;
+/**
+ * Apply accepted changes to the file's text. Pure: reads nothing, writes
+ * nothing, so the command and the tests share it.
+ */
+export declare function applyChanges(original: string, changes: ClaudeMdChange[]): ApplyResult;
+//# sourceMappingURL=claude-md.d.ts.map

package/dist/brain/claude-md.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"claude-md.d.ts","sourceRoot":"","sources":["../../src/brain/claude-md.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AACH,OAAO,EAAc,KAAK,SAAS,EAAE,MAAM,WAAW,CAAC;AAEvD,8CAA8C;AAC9C,MAAM,WAAW,cAAc;IAC7B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,GAAG,KAAK,CAAC;IACrB,qEAAqE;IACrE,OAAO,EAAE,MAAM,CAAC;IAChB,wDAAwD;IACxD,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,6DAA6D;IAC7D,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,YAAY;IAC3B,wEAAwE;IACxE,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,cAAc,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,4BAA4B;IAC5B,OAAO,EAAE,cAAc,EAAE,CAAC;IAC1B,yEAAyE;IACzE,OAAO,EAAE,cAAc,EAAE,CAAC;IAC1B,iEAAiE;IACjE,OAAO,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,cAAc,CAAC;QAAC,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACzD;AAED,mEAAmE;AACnE,wBAAsB,oBAAoB,CACxC,IAAI,EAAE,SAAS,EACf,SAAS,GAAE,OAAO,KAAa,GAC9B,OAAO,CAAC,YAAY,GAAG;IAAE,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,CAiB3C;AAED,4EAA4E;AAC5E,wBAAsB,WAAW,CAAC,IAAI,EAAE,SAAS,EAAE,GAAG,EAAE,MAAM,EAAE,EAAE,SAAS,GAAE,OAAO,KAAa,GAAG,OAAO,CAAC,OAAO,CAAC,CAsBnH;AAgDD;;;GAGG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,cAAc,EAAE,GAAG,WAAW,CAgErF"}

package/dist/brain/claude-md.js

@@ -0,0 +1,170 @@
+/**
+ * `graft claude-md pull`: write the CLAUDE.md changes accepted in Trail into
+ * this checkout's instruction file.
+ *
+ * Trail compares the repository's CLAUDE.md with what its history says and
+ * suggests edits and new sections; a person accepts some of them on the brain's
+ * CLAUDE.md page. This fetches the accepted ones, applies them to the local
+ * file, and tells Trail which it wrote so the page stops listing them.
+ *
+ * The file is edited line by line, never regenerated, so everything a change
+ * does not touch comes back byte for byte. An edit whose text is no longer in
+ * its section means the local file has moved on since Trail read it; that
+ * change is reported and left, never guessed at. Same rules as Trail's own
+ * ComposeClaudeMd, which is what the page's preview shows.
+ */
+import { baseUrlFor } from "./link.js";
+/** GET /api/public/brains/:id/claude-md — the accepted changes. */
+export async function fetchAcceptedChanges(link, fetchImpl = fetch) {
+    const url = `${baseUrlFor(link)}/api/public/brains/${encodeURIComponent(link.brainId)}/claude-md`;
+    try {
+        const res = await fetchImpl(url, {
+            headers: { authorization: `Bearer ${link.token}`, accept: "application/json" },
+            signal: AbortSignal.timeout(15_000),
+        });
+        const body = await res.text();
+        if (res.status === 404 || res.status === 503) {
+            return { error: "this brain has no CLAUDE.md suggestions yet — its Trail may be older than the feature" };
+        }
+        if (!res.ok)
+            return { error: `Trail refused the pull: ${res.status} ${body.slice(0, 200)}` };
+        const parsed = JSON.parse(body);
+        return { path: parsed.path ?? "", head_sha: parsed.head_sha ?? "", changes: parsed.changes ?? [] };
+    }
+    catch (e) {
+        return { error: `could not reach Trail: ${e instanceof Error ? e.message : e}` };
+    }
+}
+/** POST /api/public/brains/:id/claude-md/applied — what this pull wrote. */
+export async function markApplied(link, ids, fetchImpl = fetch) {
+    if (ids.length === 0)
+        return true;
+    const url = `${baseUrlFor(link)}/api/public/brains/${encodeURIComponent(link.brainId)}/claude-md/applied`;
+    try {
+        // Trail takes at most 100 per request.
+        for (let i = 0; i < ids.length; i += 100) {
+            const res = await fetchImpl(url, {
+                method: "POST",
+                headers: {
+                    authorization: `Bearer ${link.token}`,
+                    "content-type": "application/json",
+                    accept: "application/json",
+                },
+                body: JSON.stringify({ ids: ids.slice(i, i + 100) }),
+                signal: AbortSignal.timeout(15_000),
+            });
+            if (!res.ok)
+                return false;
+        }
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+const HEADING = /^(#{1,6})\s+(.+?)\s*#*\s*$/;
+/** Every ATX heading outside code fences, with the lines it owns. */
+function sectionsOf(lines) {
+    const heads = [];
+    let fence = false;
+    lines.forEach((ln, i) => {
+        const t = ln.trim();
+        if (t.startsWith("```") || t.startsWith("~~~")) {
+            fence = !fence;
+            return;
+        }
+        if (fence)
+            return;
+        const m = HEADING.exec(ln);
+        if (m)
+            heads.push({ line: i, level: m[1].length, title: m[2].trim() });
+    });
+    return heads.map((h, i) => {
+        let end = lines.length;
+        for (let j = i + 1; j < heads.length; j++) {
+            if (heads[j].level <= h.level) {
+                end = heads[j].line;
+                break;
+            }
+        }
+        return { title: h.title, level: h.level, head: h.line, end };
+    });
+}
+const norm = (s) => s.trim().toLowerCase();
+/** Trim the blank lines a section ends with, so appended text sits under its content. */
+function lastContentLine(lines, s) {
+    let i = s.end;
+    while (i > s.head + 1 && lines[i - 1].trim() === "")
+        i--;
+    return i;
+}
+/**
+ * Apply accepted changes to the file's text. Pure: reads nothing, writes
+ * nothing, so the command and the tests share it.
+ */
+export function applyChanges(original, changes) {
+    const crlf = original.includes("\r\n");
+    let lines = original.replace(/\r\n/g, "\n").split("\n");
+    const out = { text: original, written: [], present: [], skipped: [] };
+    // Edits first, against headings that exist; then additions, which may go
+    // after a section an edit just touched.
+    const ordered = [...changes.filter((c) => c.kind === "edit"), ...changes.filter((c) => c.kind === "add")];
+    for (const c of ordered) {
+        const sections = sectionsOf(lines);
+        if (c.kind === "edit") {
+            const s = sections.find((x) => norm(x.title) === norm(c.heading));
+            if (!s) {
+                out.skipped.push({ change: c, why: `no “${c.heading}” section in the file` });
+                continue;
+            }
+            const body = lines.slice(s.head + 1, s.end).join("\n");
+            const text = c.text.replace(/\r\n/g, "\n");
+            const find = (c.find ?? "").replace(/\r\n/g, "\n");
+            if (text.trim() && body.includes(text.trim())) {
+                out.present.push(c);
+                continue;
+            }
+            if (!find) {
+                const at = lastContentLine(lines, s);
+                lines = [...lines.slice(0, at), ...text.trimEnd().split("\n"), ...lines.slice(at)];
+                out.written.push(c);
+                continue;
+            }
+            const idx = body.indexOf(find);
+            if (idx < 0) {
+                out.skipped.push({ change: c, why: `the text it rewrites is no longer in “${c.heading}”` });
+                continue;
+            }
+            const next = body.slice(0, idx) + text + body.slice(idx + find.length);
+            lines = [...lines.slice(0, s.head + 1), ...next.split("\n"), ...lines.slice(s.end)];
+            out.written.push(c);
+            continue;
+        }
+        // add
+        if (sections.some((x) => norm(x.title) === norm(c.heading))) {
+            out.present.push(c);
+            continue;
+        }
+        const block = [`## ${c.heading.trim()}`, "", ...c.text.replace(/\r\n/g, "\n").trim().split("\n")];
+        const after = c.after_heading ? sections.find((x) => norm(x.title) === norm(c.after_heading)) : undefined;
+        if (after) {
+            const at = lastContentLine(lines, after);
+            // A blank line either side, whatever the file had there.
+            const tail = lines.slice(at);
+            lines = [...lines.slice(0, at), "", ...block, ...(tail.length > 0 && tail[0].trim() !== "" ? [""] : []), ...tail];
+        }
+        else {
+            while (lines.length > 0 && lines[lines.length - 1].trim() === "")
+                lines.pop();
+            lines = lines.length > 0 ? [...lines, "", ...block] : block;
+            lines.push("");
+        }
+        out.written.push(c);
+    }
+    let text = lines.join("\n");
+    if (out.written.length > 0 && !text.endsWith("\n"))
+        text += "\n";
+    out.text = out.written.length > 0 ? (crlf ? text.replace(/\n/g, "\r\n") : text) : original;
+    return out;
+}
+//# sourceMappingURL=claude-md.js.map

package/dist/brain/claude-md.js.map

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package/dist/brain/connect.d.ts

@@ -5,7 +5,7 @@
 import { type BrainLink, type BrainRule } from './link.js';
 import { type BrainWrite } from './wire.js';
 /**
- * Parse the `--brain` value.
+ * Parse the `--trail` value.
  *
  * The onboarding page hands over one string so there is one thing to copy. Two
  * accepted shapes:
@@ -33,7 +33,7 @@ export interface ConnectResult {
  *
  * The link is stored even when the pull fails. That is deliberate: a token
  * typed correctly against a brain that is momentarily unreachable should not
- * have to be pasted again — `graft brain pull` retries, and `ask` degrades to
+ * have to be pasted again — `graft trail pull` retries, and `ask` degrades to
  * the code-only answer meanwhile.
  */
 export declare function connectBrain(repo: string, link: BrainLink, opts?: {
@@ -50,7 +50,7 @@ export declare function pullBrain(repo: string, opts: {
     ids?: string[];
     fetchImpl?: typeof fetch;
 }): Promise<ConnectResult | null>;
-/** The linked brain and its cached rule set, for `graft brain status`. */
+/** The linked brain and its cached rule set, for `graft trail status`. */
 export declare function brainStatus(repo: string): {
     link: BrainLink | null;
     rules: BrainRule[];

package/dist/brain/connect.js

@@ -6,7 +6,7 @@ import { readLink, writeLink, fetchRules, writeRulesCache, readRulesCache, } fro
 import { writeBrainSections } from './wire.js';
 import { basename } from 'node:path';
 /**
- * Parse the `--brain` value.
+ * Parse the `--trail` value.
  *
  * The onboarding page hands over one string so there is one thing to copy. Two
  * accepted shapes:
@@ -21,19 +21,19 @@ import { basename } from 'node:path';
 export function parseBrainArg(value) {
     const raw = value.trim();
     if (!raw)
-        return { error: 'empty --brain value' };
+        return { error: 'empty --trail value' };
     const cut = raw.indexOf(':');
     if (cut > 0) {
         const brainId = raw.slice(0, cut).trim();
         const token = raw.slice(cut + 1).trim();
         if (!brainId || !token)
-            return { error: 'expected --brain <brainId>:<token>' };
+            return { error: 'expected --trail <brainId>:<token>' };
         return { brainId, token };
     }
     const envToken = process.env.GRAFT_BRAIN_TOKEN;
     if (!envToken) {
         return {
-            error: 'expected --brain <brainId>:<token>, or a bare brain id with the token in GRAFT_BRAIN_TOKEN',
+            error: 'expected --trail <brainId>:<token>, or a bare brain id with the token in GRAFT_BRAIN_TOKEN',
         };
     }
     return { brainId: raw, token: envToken };
@@ -43,7 +43,7 @@ export function parseBrainArg(value) {
  *
  * The link is stored even when the pull fails. That is deliberate: a token
  * typed correctly against a brain that is momentarily unreachable should not
- * have to be pasted again — `graft brain pull` retries, and `ask` degrades to
+ * have to be pasted again — `graft trail pull` retries, and `ask` degrades to
  * the code-only answer meanwhile.
  */
 export async function connectBrain(repo, link, opts = { home: '' }) {
@@ -54,7 +54,7 @@ export async function connectBrain(repo, link, opts = { home: '' }) {
             linked: true,
             ruleCount: 0,
             writes: [],
-            warning: 'could not reach the brain to pull its rules — the link is saved; run `graft brain pull` to retry',
+            warning: 'could not reach the brain to pull its rules — the link is saved; run `graft trail pull` to retry',
         };
     }
     writeRulesCache(repo, { brainId: link.brainId, fetchedAt: Date.now(), rules });
@@ -71,7 +71,7 @@ export async function pullBrain(repo, opts) {
         return null;
     return connectBrain(repo, link, opts);
 }
-/** The linked brain and its cached rule set, for `graft brain status`. */
+/** The linked brain and its cached rule set, for `graft trail status`. */
 export function brainStatus(repo) {
     const link = readLink(repo);
     const cache = readRulesCache(repo);

package/dist/brain/link.d.ts

@@ -48,7 +48,14 @@ export interface BrainLink {
  * attach a brain without writing to the checkout.
  */
 export declare function readLink(dir: string): BrainLink | null;
-/** Persist the link for repo `dir`, merging into any existing build config. */
+/** Persist the link for repo `dir`, merging into any existing build config.
+ *
+ * The write is what creates `.graft/config.json`, and that file holds the read
+ * token — which is exactly why this is also where it gets ignored. The comment
+ * on {@link BrainLink} has claimed `.graft/` was "git-ignored" since the day it
+ * was written, and nothing ever made it true: `ensureGitignored` only ever ran
+ * for the graph cache. Every repository anyone ran `graft trail connect` in was
+ * therefore one `git add -A` away from publishing a credential. */
 export declare function writeLink(dir: string, link: BrainLink): void;
 /** Forget the link for repo `dir`. Leaves the cached rules for `uninstall` to remove. */
 export declare function clearLink(dir: string): void;

package/dist/brain/link.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"link.d.ts","sourceRoot":"","sources":["../../src/brain/link.ts"],"names":[],"mappings":"AAsBA,uEAAuE;AACvE,eAAO,MAAM,YAAY,QAAqB,CAAC;AAE/C;;;;;;;;;GASG;AACH,eAAO,MAAM,kBAAkB,QAAgB,CAAC;AAEhD,kEAAkE;AAClE,MAAM,WAAW,SAAS;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,iDAAiD;IACjD,MAAM,EAAE,MAAM,CAAC;IACf,0EAA0E;IAC1E,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,EAAE,MAAM,CAAC;IACb,mEAAmE;IACnE,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,mEAAmE;AACnE,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,SAAS,EAAE,CAAC;IACnB;;;iEAG6D;IAC7D,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,gCAAgC;AAChC,MAAM,WAAW,SAAS;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,wEAAwE;IACxE,KAAK,EAAE,MAAM,CAAC;IACd,kEAAkE;IAClE,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;;;;GAKG;AACH,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAStD;AAED;;;;;;;mEAOmE;AACnE,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,GAAG,IAAI,CAG5D;AAED,yFAAyF;AACzF,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAE3C;AAED,8EAA8E;AAC9E,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAElD;AAED,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI,CAE7D;AAED,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,UAAU,GAAG,IAAI,CAEpE;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,UAAU,GAAG,IAAI,EAAE,GAAG,SAAa,GAAG,OAAO,CAIhF;AAED,2EAA2E;AAC3E,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,SAAa,GAAG,IAAI,CAIpE;AAED;;;GAGG;AACH,wBAAgB,UAAU,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAElD;AAeD;;;;;;GAMG;AACH,wBAAsB,UAAU,CAC9B,IAAI,EAAE,SAAS,EACf,SAAS,GAAE,OAAO,KAAa,GAC9B,OAAO,CAAC,SAAS,EAAE,GAAG,IAAI,CAAC,CA4B7B"}

package/dist/brain/link.js

@@ -14,6 +14,8 @@
  */
 import { readBuildConfig, patchBuildConfig, cacheDir, readJson, writeJsonAtomic } from '../util/state.js';
 import { join } from 'node:path';
+import { ensureGitignored, LINK_NOTE } from '../context/node-file.js';
+import { BUILD_CONFIG_DIR } from '../util/state.js';
 /** Default API host. Overridden by GRAFT_BRAIN_URL, for staging and self-hosted. */
 const DEFAULT_BRAIN_BASE_URL = 'https://agents.nanonets.com';
 /** How long a cached rule set is served before upkeep refreshes it. */
@@ -46,9 +48,17 @@ export function readLink(dir) {
         return null;
     return stored;
 }
-/** Persist the link for repo `dir`, merging into any existing build config. */
+/** Persist the link for repo `dir`, merging into any existing build config.
+ *
+ * The write is what creates `.graft/config.json`, and that file holds the read
+ * token — which is exactly why this is also where it gets ignored. The comment
+ * on {@link BrainLink} has claimed `.graft/` was "git-ignored" since the day it
+ * was written, and nothing ever made it true: `ensureGitignored` only ever ran
+ * for the graph cache. Every repository anyone ran `graft trail connect` in was
+ * therefore one `git add -A` away from publishing a credential. */
 export function writeLink(dir, link) {
     patchBuildConfig(dir, { brain: link });
+    ensureGitignored(dir, join(dir, BUILD_CONFIG_DIR), LINK_NOTE);
 }
 /** Forget the link for repo `dir`. Leaves the cached rules for `uninstall` to remove. */
 export function clearLink(dir) {