@monoes/monograph 1.6.12 → 1.6.15

package/dist/src/mcp-tools/resolve-node.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"resolve-node.js","sourceRoot":"","sources":["../../../src/mcp-tools/resolve-node.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AAkBxD,oFAAoF;AACpF,MAAM,CAAC,MAAM,aAAa,GAAG,EAAE,CAAC;AAChC,uFAAuF;AACvF,MAAM,cAAc,GAAG,GAAG,CAAC;AAE3B,MAAM,UAAU,WAAW,CAAC,GAA4B;IACtD,OAAO;QACL,EAAE,EAAE,GAAG,CAAC,EAAY;QACpB,IAAI,EAAE,GAAG,CAAC,IAAc;QACxB,KAAK,EAAE,GAAG,CAAC,KAAe;QAC1B,QAAQ,EAAG,GAAG,CAAC,SAA2B,IAAI,IAAI;QAClD,SAAS,EAAG,GAAG,CAAC,UAA4B,IAAI,IAAI;KACrD,CAAC;AACJ,CAAC;AAED,4FAA4F;AAC5F,MAAM,UAAU,eAAe,CAAC,GAA4B,EAAE,QAAgB;IAC5E,MAAM,OAAO,GAAI,GAAG,CAAC,SAA2B,IAAI,EAAE,CAAC;IACvD,OAAO,OAAO,KAAK,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;AAC5D,CAAC;AAED,MAAM,SAAS,GAAG,CAAC,GAA4B,EAAW,EAAE,CAC1D,UAAU,CAAE,GAAG,CAAC,SAA2B,IAAI,EAAE,CAAC,CAAC;AAErD;;;;GAIG;AACH,MAAM,UAAU,iBAAiB,CAC/B,EAAqB,EACrB,IAAY,EACZ,QAAiB;IAEjB,MAAM,IAAI,GAAG,EAAE;SACZ,OAAO,CAAC,4CAA4C,CAAC;SACrD,GAAG,CAAC,IAAI,EAAE,cAAc,CAA8B,CAAC;IAC1D,IAAI,OAAO,GAAG,IAAI,CAAC;IACnB,IAAI,QAAQ,EAAE,CAAC;QACb,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,QAAQ,CAAC,CAAC;QAC3D,OAAO,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,eAAe,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC;IACxF,CAAC;IAED,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC;IACpD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC;IAErE,MAAM,MAAM,GAAG,CAAC,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC;IACvF,OAAO,EAAE,UAAU,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,aAAa,CAAC,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,CAAC;AACzE,CAAC"}

package/dist/src/pipeline/build-lock.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"build-lock.d.ts","sourceRoot":"","sources":["../../../src/pipeline/build-lock.ts"],"names":[],"mappings":"AAkBA,MAAM,WAAW,eAAe;IAC9B,GAAG,EAAE,MAAM,CAAC;IACZ,gDAAgD;IAChD,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,MAAM,SAAS,GACjB;IAAE,QAAQ,EAAE,IAAI,CAAC;IAAC,OAAO,EAAE,MAAM,IAAI,CAAA;CAAE,GACvC;IAAE,QAAQ,EAAE,KAAK,CAAC;IAAC,MAAM,EAAE,eAAe,GAAG,IAAI,CAAA;CAAE,CAAC;AAExD,eAAO,MAAM,aAAa,WAAY,MAAM,KAAG,MAAgC,CAAC;AA6ChF,4FAA4F;AAC5F,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,eAAe,GAAG,IAAI,CAG1E;AAED,uEAAuE;AACvE,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,eAAe,GAAG,MAAM,CASvE;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAiE1D"}
+{"version":3,"file":"build-lock.d.ts","sourceRoot":"","sources":["../../../src/pipeline/build-lock.ts"],"names":[],"mappings":"AA6CA,MAAM,WAAW,eAAe;IAC9B,GAAG,EAAE,MAAM,CAAC;IACZ,gDAAgD;IAChD,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,MAAM,SAAS,GACjB;IAAE,QAAQ,EAAE,IAAI,CAAC;IAAC,OAAO,EAAE,MAAM,IAAI,CAAA;CAAE,GACvC;IAAE,QAAQ,EAAE,KAAK,CAAC;IAAC,MAAM,EAAE,eAAe,GAAG,IAAI,CAAA;CAAE,CAAC;AAExD,eAAO,MAAM,aAAa,WAAY,MAAM,KAAG,MAAgC,CAAC;AAsDhF,4FAA4F;AAC5F,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,eAAe,GAAG,IAAI,CAG1E;AAED,uEAAuE;AACvE,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,eAAe,GAAG,MAAM,CASvE;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAiE1D"}

package/dist/src/pipeline/build-lock.js

@@ -1,4 +1,4 @@
-import { mkdirSync, readFileSync, statSync, unlinkSync, utimesSync, writeFileSync } from 'node:fs';
+import { mkdirSync, readFileSync, readlinkSync, statSync, unlinkSync, utimesSync, writeFileSync, } from 'node:fs';
 import { uptime } from 'node:os';
 import { dirname } from 'node:path';
 // Cross-process build mutex. Callers arrive from several independent entry points
@@ -12,14 +12,33 @@ import { dirname } from 'node:path';
 // nobody has refreshed it for STALE_AFTER_MS (#340). The holder touches it
 // every HEARTBEAT_MS whenever the build yields the event loop, so a long build
 // is not taken over for its age alone.
+//
+// #370: lines 3 and 4 hold the holder's pid namespace and boot id. A pid only
+// means something inside its own pid namespace — sandboxed tools (bwrap
+// --unshare-pid) give every command a fresh one with tiny, reused pids, so a
+// killed sandboxed build left "pid 47", and in the next sandbox some other
+// process was pid 47. A lock from another boot is stale; one from another
+// namespace can't be checked by pid, so it is stale once its heartbeat has
+// been silent for FOREIGN_STALE_AFTER_MS.
 const HEARTBEAT_MS = 30_000;
 const STALE_AFTER_MS = 30 * 60_000;
+const FOREIGN_STALE_AFTER_MS = 4 * HEARTBEAT_MS;
+function readIdentity(file, link) {
+    try {
+        return (link ? readlinkSync(file) : readFileSync(file, 'utf8')).trim();
+    }
+    catch {
+        return ''; // no /proc (macOS, Windows): unknown, compared as equal
+    }
+}
+const ownPidNamespace = readIdentity('/proc/self/ns/pid', true);
+const ownBootId = readIdentity('/proc/sys/kernel/random/boot_id', false);
 export const buildLockPath = (dbPath) => `${dbPath}.build-lock`;
 function readLockFile(lockPath) {
     try {
         const raw = readFileSync(lockPath, 'utf8');
         const { mtimeMs } = statSync(lockPath);
-        const [pidLine = '', startedLine = ''] = raw.split('\n');
+        const [pidLine = '', startedLine = '', nsLine = '', bootLine = ''] = raw.split('\n');
         const startedAt = Number.parseInt(startedLine, 10);
         return {
             raw,
@@ -29,6 +48,8 @@ function readLockFile(lockPath) {
                 startedAt: Number.isFinite(startedAt) ? startedAt : mtimeMs,
                 lockPath,
             },
+            pidNamespace: nsLine.trim(),
+            bootId: bootLine.trim(),
         };
     }
     catch {
@@ -48,6 +69,11 @@ function isPidAlive(pid) {
     }
 }
 function isStale(lock) {
+    if (lock.bootId && ownBootId && lock.bootId !== ownBootId)
+        return true;
+    if (lock.pidNamespace && ownPidNamespace && lock.pidNamespace !== ownPidNamespace) {
+        return Date.now() - lock.mtimeMs > FOREIGN_STALE_AFTER_MS;
+    }
     if (!isPidAlive(lock.holder.pid))
         return true;
     const bootedAt = Date.now() - uptime() * 1000;
@@ -71,7 +97,7 @@ export function describeBuildLockHolder(holder) {
 export function acquireBuildLock(dbPath) {
     const lockPath = buildLockPath(dbPath);
     mkdirSync(dirname(lockPath), { recursive: true });
-    const content = `${process.pid}\n${Date.now()}\n`;
+    const content = `${process.pid}\n${Date.now()}\n${ownPidNamespace}\n${ownBootId}\n`;
     const tryCreate = () => {
         try {
             writeFileSync(lockPath, content, { flag: 'wx' });

package/dist/src/pipeline/build-lock.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/orchestrator.d.ts

@@ -6,6 +6,12 @@ export interface BuildOptions extends Partial<PipelineOptions> {
     force?: boolean;
     /** When true, skip the full rebuild if the index is already fresh (matches HEAD). Default false. */
     incremental?: boolean;
+    /**
+     * Where to write GRAPH_REPORT.md; a relative path resolves against the repo.
+     * Defaults to $MONOGRAPH_REPORT_PATH, else `.monomind/GRAPH_REPORT.md` (#414 —
+     * pass `'GRAPH_REPORT.md'` for the pre-#414 repo-root location).
+     */
+    reportPath?: string;
 }
 /**
  * What a build call actually did. A resolved promise alone does not mean the

package/dist/src/pipeline/orchestrator.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AACvE,OAAO,EAAoB,KAAK,eAAe,EAA2B,MAAM,iBAAiB,CAAC;AA2BlG,OAAO,KAAK,EAAmB,eAAe,EAAE,MAAM,YAAY,CAAC;AAgBnE,MAAM,WAAW,YAAa,SAAQ,OAAO,CAAC,eAAe,CAAC;IAC5D,UAAU,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB,KAAK,IAAI,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,oGAAoG;IACpG,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;;;;OAIG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;GAKG;AACH,MAAM,MAAM,WAAW,GACnB;IACE,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IACzC,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAC1C,GACD;IACE,MAAM,EAAE,SAAS,CAAC;IAClB,MAAM,EAAE,QAAQ,GAAG,OAAO,CAAC;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,wEAAwE;IACxE,MAAM,CAAC,EAAE,eAAe,CAAC;CAC1B,CAAC;AAQN,wBAAsB,UAAU,CAC9B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,CAAC,CAiBtB;AAsQD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,qBAAqB,CACzC,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EAAE,EACzB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,GAAG,IAAI,CAAC,CAa7B"}

package/dist/src/pipeline/orchestrator.js

@@ -35,7 +35,12 @@ import { PipelineRunner } from './runner.js';
 import { DEFAULT_OPTIONS } from './types.js';
 function getCurrentCommitHash(repoPath) {
     try {
-        return execSync('git rev-parse HEAD', { cwd: repoPath, encoding: 'utf8' }).trim();
+        // #371: an unborn HEAD (no commits yet) is expected — keep git's error off the console.
+        return execSync('git rev-parse HEAD', {
+            cwd: repoPath,
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+        }).trim();
     }
     catch {
         return null;
@@ -273,7 +278,9 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
             try {
                 const suggestOut = outputs.get('suggest');
                 const questions = suggestOut?.questions ?? [];
-                await generateGraphReport(resolve(repoPath), undefined, dbPath, questions);
+                const reportOpt = options.reportPath ?? (process.env.MONOGRAPH_REPORT_PATH || undefined);
+                const reportPath = reportOpt ? resolve(repoPath, reportOpt) : undefined;
+                await generateGraphReport(resolve(repoPath), reportPath, dbPath, questions);
             }
             catch {
                 // Report generation is non-fatal — the build itself already committed.

package/dist/src/pipeline/orchestrator.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/god-nodes.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"god-nodes.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/god-nodes.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,OAAO,EAAiB,MAAM,gBAAgB,CAAC;AAC7D,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAkBjD,MAAM,MAAM,eAAe,GACvB,iBAAiB,GACjB,aAAa,GACb,kBAAkB,GAClB,eAAe,GACf,iBAAiB,GACjB,aAAa,CAAC;AAElB,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,CAAC,OAAO,GAAG;QAAE,QAAQ,EAAE,eAAe,CAAC;QAAC,mBAAmB,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC,EAAE,CAAC;IACjG,UAAU,EAAE,kBAAkB,CAAC;CAChC;AAQD,eAAO,MAAM,aAAa,EAAE,aAAa,CAAC,cAAc,CA8EvD,CAAC;AAEF;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,cAAc,GAAG,MAAM,CA+B7D"}

package/dist/src/pipeline/phases/god-nodes.js

@@ -1,3 +1,4 @@
+import { isAnonymousClosure } from '../../storage/anonymous-closure.js';
 const EXCLUDED_LABELS = new Set(['File', 'Folder', 'Community', 'Concept']);
 // Test files stay in the graph (useful for impact/navigation) but are excluded
 // from centrality rankings — a heavily-importing test suite is not a god node.
@@ -5,6 +6,10 @@ const TEST_PATH_RE = /(\.test\.|\.spec\.|__tests__|__mocks__)/;
 function isTestNode(n) {
     return !!(n.filePath && TEST_PATH_RE.test(n.filePath));
 }
+// Anonymous closures have no name worth reporting as a hotspot (#404).
+function isRankable(n) {
+    return !EXCLUDED_LABELS.has(n.label) && !isTestNode(n) && !isAnonymousClosure(n);
+}
 function percentile(sorted, p) {
     if (sorted.length === 0)
         return 0;
@@ -29,7 +34,7 @@ export const godNodesPhase = {
         const allFanIn = [];
         const allFanOut = [];
         for (const n of symbolNodes) {
-            if (EXCLUDED_LABELS.has(n.label) || isTestNode(n))
+            if (!isRankable(n))
                 continue;
             allFanIn.push(inDeg.get(n.id) ?? 0);
             allFanOut.push(outDeg.get(n.id) ?? 0);
@@ -47,9 +52,7 @@ export const godNodesPhase = {
         const p75FanIn = thresholds.p75FanIn;
         const p75FanOut = thresholds.p75FanOut;
         const godNodes = symbolNodes
-            .filter((n) => !EXCLUDED_LABELS.has(n.label) &&
-            !isTestNode(n) &&
-            (inDeg.get(n.id) ?? 0) + (outDeg.get(n.id) ?? 0) > p95FanIn)
+            .filter((n) => isRankable(n) && (inDeg.get(n.id) ?? 0) + (outDeg.get(n.id) ?? 0) > p95FanIn)
             .map((n) => {
             const fanIn = inDeg.get(n.id) ?? 0;
             const fanOut = outDeg.get(n.id) ?? 0;

package/dist/src/pipeline/phases/god-nodes.js.map

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package/dist/src/pipeline/phases/scan.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scan.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/scan.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AA8DjD,MAAM,WAAW,UAAU;IACzB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,eAAO,MAAM,SAAS,EAAE,aAAa,CAAC,UAAU,CAiG/C,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,IAAI,GAAG,MAAM,GAAG,MAAM,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;CACjB;AAOD,wBAAgB,YAAY,CAAC,IAAI,EAAE;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAA;CAAE,GAAG,gBAAgB,CAe9F"}
+{"version":3,"file":"scan.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/scan.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAsGjD,MAAM,WAAW,UAAU;IACzB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,eAAO,MAAM,SAAS,EAAE,aAAa,CAAC,UAAU,CAyG/C,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,IAAI,GAAG,MAAM,GAAG,MAAM,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;CACjB;AAOD,wBAAgB,YAAY,CAAC,IAAI,EAAE;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAA;CAAE,GAAG,gBAAgB,CAe9F"}

package/dist/src/pipeline/phases/scan.js

@@ -1,3 +1,4 @@
+import { execFileSync } from 'node:child_process';
 import { existsSync, lstatSync, readdirSync, readFileSync } from 'node:fs';
 import { extname, join } from 'node:path';
 import micromatch from 'micromatch';
@@ -26,6 +27,15 @@ const DEFAULT_IGNORE = new Set([
     '.vercel',
     '.wrangler',
     '.open-next',
+    // Platform asset mirrors `monomind init` writes next to .claude/, the
+    // monograph cache and the agent mail dir — never user source (#404).
+    '.agents',
+    '.gemini',
+    '.kimi-code',
+    '.opencode',
+    '.codex',
+    '.monograph',
+    '.mail',
 ]);
 const BINARY_EXTENSIONS = new Set([
     '.png',
@@ -55,11 +65,39 @@ const GENERATED_PATTERNS = [
     /\.min\.(js|css)$/,
     /\.pb\.go$/,
     /_generated\.ts$/,
-    // Monograph's own build output (reporting/graph-report.ts writes it to the repo
-    // root). Indexing it feeds a previous build's prose back into the graph as
+    // Monograph's own build output (written to the repo root before #414, and still
+    // when a build passes reportPath: 'GRAPH_REPORT.md'). Indexing it feeds a previous build's prose back into the graph as
     // document nodes and edges, compounding on every rebuild.
     /^GRAPH_REPORT\.md$/,
 ];
+/**
+ * Files git would consider part of the working tree under `repoPath` (tracked
+ * plus untracked-but-not-ignored), relative to `repoPath`, and every ancestor
+ * directory of those files. Returns null outside a git work tree or when git
+ * is unavailable, so the scan falls back to walking everything.
+ */
+function listGitVisible(repoPath) {
+    let out;
+    try {
+        out = execFileSync('git', ['-C', repoPath, 'ls-files', '-z', '--cached', '--others', '--exclude-standard'], { encoding: 'utf8', maxBuffer: 512 * 1024 * 1024, stdio: ['ignore', 'pipe', 'ignore'] });
+    }
+    catch {
+        return null;
+    }
+    const files = new Set();
+    const dirs = new Set();
+    for (const raw of out.split('\0')) {
+        // A trailing slash marks a nested repository/submodule git does not descend into.
+        const rel = raw.endsWith('/') ? raw.slice(0, -1) : raw;
+        if (!rel)
+            continue;
+        files.add(rel);
+        for (let i = rel.indexOf('/'); i !== -1; i = rel.indexOf('/', i + 1)) {
+            dirs.add(rel.slice(0, i));
+        }
+    }
+    return { files, dirs };
+}
 export const scanPhase = {
     name: 'scan',
     deps: [],
@@ -85,7 +123,13 @@ export const scanPhase = {
                 }
             }
         }
-        function walk(dir) {
+        // Honour .gitignore: inside a git work tree only files git lists are scanned.
+        const gitVisible = listGitVisible(ctx.repoPath);
+        const relOf = (fullPath) => fullPath.slice(ctx.repoPath.length + 1).replace(/\\/g, '/');
+        const isRescued = (rel) => negationPatterns.length > 0 && micromatch.isMatch(rel, negationPatterns, { dot: true });
+        // `gitFiltered` is false below a submodule or nested repo, which git lists
+        // as a single entry — everything inside it is walked as before.
+        function walk(dir, gitFiltered = gitVisible !== null) {
             let dirents;
             try {
                 dirents = readdirSync(dir, { withFileTypes: true });
@@ -114,21 +158,25 @@ export const scanPhase = {
                 catch {
                     continue;
                 }
+                const rel = relOf(fullPath);
                 if (stat.isDirectory()) {
-                    // Always traverse directories — negation patterns may rescue files inside ignored dirs
-                    walk(fullPath);
+                    if (!gitVisible || !gitFiltered)
+                        walk(fullPath, false);
+                    else if (gitVisible.files.has(rel))
+                        walk(fullPath, false);
+                    // Skip wholly gitignored trees (venvs, caches) unless a negation
+                    // pattern could rescue something inside them.
+                    else if (gitVisible.dirs.has(rel) || negationPatterns.length > 0)
+                        walk(fullPath, true);
                     continue;
                 }
+                if (gitVisible && gitFiltered && !gitVisible.files.has(rel) && !isRescued(rel))
+                    continue;
                 if (ignorePatterns.length > 0) {
-                    const rel = fullPath.slice(ctx.repoPath.length + 1);
                     const isIgnored = micromatch.isMatch(rel, ignorePatterns, { dot: true });
                     const isDirIgnored = micromatch.isMatch(rel, ignorePatterns.map((p) => (p.endsWith('/') ? `${p}**` : p)), { dot: true });
-                    if (isIgnored || isDirIgnored) {
-                        const isNegated = negationPatterns.length > 0 &&
-                            micromatch.isMatch(rel, negationPatterns, { dot: true });
-                        if (!isNegated)
-                            continue;
-                    }
+                    if ((isIgnored || isDirIgnored) && !isRescued(rel))
+                        continue;
                 }
                 const ext = extname(entry).toLowerCase();
                 if (BINARY_EXTENSIONS.has(ext))

package/dist/src/pipeline/phases/scan.js.map

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package/dist/src/reporting/graph-report.js

@@ -1,5 +1,5 @@
-import { writeFileSync } from 'node:fs';
-import { join } from 'node:path';
+import { mkdirSync, writeFileSync } from 'node:fs';
+import { dirname, join } from 'node:path';
 import { checkStaleness } from '../staleness/git-staleness.js';
 import { closeDb, openDb } from '../storage/db.js';
 function queryNodesByType(db) {
@@ -287,7 +287,8 @@ export function generateGraphReport(dbOrRepoPath, outputPath, dbPath, questions
     // Async overload: first arg is a repo path string
     const repoPath = dbOrRepoPath;
     const resolvedDbPath = dbPath ?? join(repoPath, '.monograph', 'graph.db');
-    const resolvedOutputPath = outputPath ?? join(repoPath, 'GRAPH_REPORT.md');
+    // #414: under .monomind/, not the user's repo root, unless the caller asks.
+    const resolvedOutputPath = outputPath ?? join(repoPath, '.monomind', 'GRAPH_REPORT.md');
     return (async () => {
         const db = openDb(resolvedDbPath);
         try {
@@ -311,6 +312,7 @@ export function generateGraphReport(dbOrRepoPath, outputPath, dbPath, questions
             const confidenceSection = buildConfidenceAuditSection(db);
             const gapSection = buildKnowledgeGapSection(db);
             const markdown = buildMarkdownWithQuestions(nodeCount, edgeCount, nodesByType, edgesByRelation, topNodes, communities, staleFiles, questions, confidenceSection) + (gapSection ? `\n${gapSection}` : '');
+            mkdirSync(dirname(resolvedOutputPath), { recursive: true });
             writeFileSync(resolvedOutputPath, markdown, 'utf8');
             return {
                 markdown,

package/dist/src/reporting/graph-report.js.map

@@ -1 +1 @@
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package/dist/src/staleness/git-staleness.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"git-staleness.d.ts","sourceRoot":"","sources":["../../../src/staleness/git-staleness.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD;;;;;;;;;;;;GAYG;AACH,MAAM,MAAM,mBAAmB,GAAG,OAAO,GAAG,OAAO,GAAG,UAAU,GAAG,SAAS,GAAG,SAAS,CAAC;AAKzF,MAAM,WAAW,eAAe;IAC9B;;;;;;OAMG;IACH,OAAO,EAAE,OAAO,CAAC;IACjB,iEAAiE;IACjE,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,kDAAkD;IAClD,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,0CAA0C;IAC1C,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAE1B,6DAA6D;IAC7D,KAAK,EAAE,mBAAmB,CAAC;IAC3B,+EAA+E;IAC/E,MAAM,EAAE,MAAM,CAAC;IACf,+EAA+E;IAC/E,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,sFAAsF;IACtF,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,0EAA0E;IAC1E,aAAa,EAAE,OAAO,GAAG,IAAI,CAAC;IAC9B,qEAAqE;IACrE,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,gEAAgE;IAChE,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9B,2EAA2E;IAC3E,cAAc,EAAE,MAAM,EAAE,GAAG,IAAI,CAAC;IAChC,2EAA2E;IAC3E,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,wDAAwD;IACxD,eAAe,EAAE,OAAO,CAAC;IACzB,0EAA0E;IAC1E,eAAe,EAAE,OAAO,CAAC;CAC1B;AAoJD,wBAAgB,cAAc,CAAC,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,GAAG,eAAe,CA4HjF"}

package/dist/src/staleness/git-staleness.js

@@ -53,6 +53,7 @@ function checkDirtyWorktree(repoPath) {
             cwd: repoPath,
             encoding: 'utf8',
             maxBuffer: 8 * 1024 * 1024,
+            stdio: ['ignore', 'pipe', 'pipe'], // #371
         });
         // Porcelain v1 lines are `XY <path>`; ignored files are excluded by default.
         const paths = out
@@ -129,7 +130,12 @@ export function checkStaleness(db, repoPath) {
     // 1. Current HEAD (full SHA — `--short` output length varies by repo size)
     let currentCommit = null;
     try {
-        currentCommit = execSync('git rev-parse HEAD', { cwd: repoPath, encoding: 'utf8' }).trim();
+        // #371: keep git's own error (unborn HEAD, not a repo) off the console.
+        currentCommit = execSync('git rev-parse HEAD', {
+            cwd: repoPath,
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+        }).trim();
     }
     catch {
         // Not a git repo, no git binary, or a broken checkout. Nothing is known

package/dist/src/staleness/git-staleness.js.map

@@ -1 +1 @@
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+{"version":3,"file":"git-staleness.js","sourceRoot":"","sources":["../../../src/staleness/git-staleness.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAC9C,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAkBhE,iGAAiG;AACjG,MAAM,cAAc,GAAG,EAAE,CAAC;AA4C1B,SAAS,QAAQ,CAAC,EAAe;IAC/B,IAAI,CAAC;QACH,MAAM,IAAI,GAAG,EAAE,CAAC,OAAO,CAAC,mCAAmC,CAAC,CAAC,GAAG,EAG7D,CAAC;QACJ,OAAO,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACpD,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,GAAG,EAAE,CAAC;IACnB,CAAC;AACH,CAAC;AAED,gFAAgF;AAChF,SAAS,aAAa,CAAC,GAAuB;IAC5C,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,CAAC;IACtB,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAC/B,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;YAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;YACjD,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC;QACzC,CAAC;IACH,CAAC;IAAC,MAAM,CAAC;QACP,6CAA6C;IAC/C,CAAC;IACD,MAAM,KAAK,GAAG,GAAG;SACd,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SACpB,MAAM,CAAC,OAAO,CAAC,CAAC;IACnB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC;AACzC,CAAC;AAED;;;;GAIG;AACH,SAAS,iBAAiB,CAAC,EAAe;IACxC,MAAM,MAAM,GAAG,OAAO,EAAE,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;IAC1D,IAAI,CAAC,MAAM,IAAI,MAAM,KAAK,UAAU;QAAE,OAAO,KAAK,CAAC;IACnD,OAAO,mBAAmB,CAAC,MAAM,CAAC,KAAK,IAAI,CAAC;AAC9C,CAAC;AAQD;;;;GAIG;AACH,SAAS,kBAAkB,CAAC,QAAgB;IAC1C,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,QAAQ,CAAC,qCAAqC,EAAE;YAC1D,GAAG,EAAE,QAAQ;YACb,QAAQ,EAAE,MAAM;YAChB,SAAS,EAAE,CAAC,GAAG,IAAI,GAAG,IAAI;YAC1B,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,OAAO;SAC3C,CAAC,CAAC;QACH,6EAA6E;QAC7E,MAAM,KAAK,GAAG,GAAG;aACd,KAAK,CAAC,IAAI,CAAC;aACX,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC;aACjC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;aACnC,MAAM,CAAC,OAAO,CAAC,CAAC;QACnB,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,cAAc,CAAC,EAAE,KAAK,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC;IACjG,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;IACjD,CAAC;AACH,CAAC;AAcD,SAAS,WAAW,CAAC,IAAyB,EAAE,KAAkB;IAChE,OAAO;QACL,OAAO,EAAE,KAAK,CAAC,OAAO;QACtB,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,IAAI;QACzC,aAAa,EAAE,KAAK,CAAC,aAAa;QAClC,aAAa,EAAE,KAAK,CAAC,aAAa;QAClC,YAAY,EAAE,KAAK,CAAC,YAAY;QAChC,UAAU,EAAE,KAAK,CAAC,UAAU;QAC5B,KAAK,EAAE,KAAK,CAAC,KAAK;QAClB,MAAM,EAAE,KAAK,CAAC,MAAM;QACpB,eAAe,EAAE,KAAK,CAAC,eAAe;QACtC,WAAW,EAAE,IAAI,CAAC,GAAG,CAAC,cAAc,CAAC,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,IAAI;QAClE,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK;QAChC,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK;QAC7B,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK;QACjC,cAAc,EAAE,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;QACtF,gBAAgB,EAAE,IAAI,CAAC,GAAG,CAAC,oBAAoB,CAAC,IAAI,IAAI;QACxD,eAAe,EAAE,KAAK,CAAC,KAAK,KAAK,UAAU;QAC3C,eAAe,EAAE,KAAK,CAAC,KAAK,KAAK,OAAO;KACzC,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,SAAS,sBAAsB,CAC7B,IAAyB,EACzB,KAAoB;IAEpB,IAAI,KAAK,CAAC,KAAK,KAAK,IAAI,EAAE,CAAC;QACzB,OAAO;YACL,KAAK,EAAE,SAAS;YAChB,MAAM,EACJ,sFAAsF;SACzF,CAAC;IACJ,CAAC;IACD,IAAI,KAAK,CAAC,KAAK,EAAE,CAAC;QAChB,OAAO;YACL,KAAK,EAAE,OAAO;YACd,MAAM,EAAE,0BAA0B,KAAK,CAAC,KAAK,8DAA8D;SAC5G,CAAC;IACJ,CAAC;IACD,MAAM,QAAQ,GAAG,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC;IACxF,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,oBAAoB,CAAC,IAAI,IAAI,CAAC;IAC5D,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO;YACL,KAAK,EAAE,SAAS;YAChB,MAAM,EAAE,kDAAkD,QAAQ,CAAC,MAAM,kDAAkD;SAC5H,CAAC;IACJ,CAAC;IACD,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO;YACL,KAAK,EAAE,SAAS;YAChB,MAAM,EAAE,8DAA8D,YAAY,EAAE;SACrF,CAAC;IACJ,CAAC;IACD,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,mDAAmD,EAAE,CAAC;AACzF,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,EAAe,EAAE,QAAgB;IAC9D,MAAM,IAAI,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAC;IAC1B,MAAM,iBAAiB,GAAG,IAAI,CAAC,GAAG,CAAC,kBAAkB,CAAC,IAAI,IAAI,CAAC;IAC/D,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,CAAC,CAAC,iBAAiB,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACpF,MAAM,QAAQ,GAAG,iBAAiB,CAAC,EAAE,CAAC,CAAC;IAEvC,2EAA2E;IAC3E,IAAI,aAAa,GAAkB,IAAI,CAAC;IACxC,IAAI,CAAC;QACH,wEAAwE;QACxE,aAAa,GAAG,QAAQ,CAAC,oBAAoB,EAAE;YAC7C,GAAG,EAAE,QAAQ;YACb,QAAQ,EAAE,MAAM;YAChB,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC;SACpC,CAAC,CAAC,IAAI,EAAE,CAAC;IACZ,CAAC;IAAC,MAAM,CAAC;QACP,wEAAwE;QACxE,mDAAmD;QACnD,OAAO,WAAW,CAAC,IAAI,EAAE;YACvB,OAAO,EAAE,KAAK;YACd,aAAa,EAAE,IAAI;YACnB,aAAa,EAAE,IAAI;YACnB,YAAY,EAAE,EAAE;YAChB,UAAU,EAAE,IAAI;YAChB,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS;YACxC,MAAM,EAAE,QAAQ;gBACd,CAAC,CAAC,kFAAkF;gBACpF,CAAC,CAAC,4HAA4H;YAChI,eAAe,EAAE,iBAAiB;YAClC,KAAK,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE;SAC/C,CAAC,CAAC;IACL,CAAC;IAED,MAAM,kBAAkB,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IACrD,MAAM,KAAK,GAAG,kBAA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package/dist/src/storage/anonymous-closure.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Anonymous closures (`() => {`, `async (req) => {`, `function () {`) become
+ * Function/Method nodes named after their first source line, since they have
+ * no name field. They stay in the graph — CALLS edges are attributed to the
+ * innermost enclosing callable, closures included — but they are noise on
+ * name-based surfaces: search results and god-node rankings (#404).
+ */
+export declare function isAnonymousClosure(node: {
+    label: string;
+    name: string;
+}): boolean;
+/** SQL twin of {@link isAnonymousClosure} for a `nodes` table aliased `n`. */
+export declare const NOT_ANONYMOUS_CLOSURE_SQL: string;
+//# sourceMappingURL=anonymous-closure.d.ts.map

package/dist/src/storage/anonymous-closure.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"anonymous-closure.d.ts","sourceRoot":"","sources":["../../../src/storage/anonymous-closure.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAOH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAAG,OAAO,CAEjF;AAED,8EAA8E;AAC9E,eAAO,MAAM,yBAAyB,QAI6C,CAAC"}