fix: remove shell syntax from run() in 4 tools

src/tools/audit-workspace.ts

@@ -1,6 +1,8 @@
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { run } from "../lib/git.js";
-import { readIfExists, findWorkspaceDocs } from "../lib/files.js";
+import { readIfExists, findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js";
+import { readdirSync } from "fs";
+import { join } from "path";
 
 /** Extract top-level work areas from file paths generically */
 function detectWorkAreas(files: string[]): Set<string> {
@@ -36,7 +38,8 @@ export function registerAuditWorkspace(server: McpServer): void {
     {},
     async () => {
       const docs = findWorkspaceDocs();
-      const recentFiles = run("git diff --name-only HEAD~10 2>/dev/null || echo ''").split("\n").filter(Boolean);
+      const diffResult = run(["diff", "--name-only", "HEAD~10"]);
+      const recentFiles = diffResult.startsWith("[") ? [] : diffResult.split("\n").filter(Boolean);
       const sections: string[] = [];
 
       // Doc freshness
@@ -75,7 +78,21 @@ export function registerAuditWorkspace(server: McpServer): void {
       // Check for gap trackers or similar tracking docs
       const trackingDocs = Object.entries(docs).filter(([n]) => /gap|track|progress/i.test(n));
       if (trackingDocs.length > 0) {
-        const testFilesCount = parseInt(run("find tests -name '*.spec.ts' -o -name '*.test.ts' 2>/dev/null | wc -l").trim()) || 0;
+        // Count test files using Node.js fs
+        let testFilesCount = 0;
+        const countTestFiles = (dir: string, depth = 0): void => {
+          if (depth > 4) return;
+          try {
+            for (const entry of readdirSync(dir, { withFileTypes: true })) {
+              if (entry.isDirectory() && !entry.name.startsWith(".") && entry.name !== "node_modules") {
+                countTestFiles(join(dir, entry.name), depth + 1);
+              } else if (entry.isFile() && /\.(spec|test)\.(ts|tsx|js|jsx)$/.test(entry.name)) {
+                testFilesCount++;
+              }
+            }
+          } catch { /* dir may not exist */ }
+        };
+        countTestFiles(join(PROJECT_DIR, "tests"));
         sections.push(`## Tracking Docs\n${trackingDocs.map(([n]) => {
           const age = docStatus.find(d => d.name === n)?.ageHours ?? "?";
           return `- .claude/${n} — last updated ${age}h ago`;

src/tools/checkpoint.ts

@@ -63,32 +63,27 @@ ${dirty || "clean"}
         const shortSummary = summary.split("\n")[0].slice(0, 72);
         const commitMsg = `checkpoint: ${shortSummary}`;
 
-        let addCmd: string;
-        switch (mode) {
-          case "staged": {
-            const staged = getStagedFiles();
-            if (!staged) {
-              commitResult = "nothing staged — skipped commit (use 'tracked' or 'all' mode, or stage files first)";
-            }
-            addCmd = "true"; // noop, already staged
-            break;
+        if (mode === "staged") {
+          const staged = getStagedFiles();
+          if (!staged) {
+            commitResult = "nothing staged — skipped commit (use 'tracked' or 'all' mode, or stage files first)";
           }
-          case "all":
-            addCmd = "git add -A";
-            break;
-          case "tracked":
-          default:
-            addCmd = "git add -u";
-            break;
         }
 
         if (commitResult === "no uncommitted changes") {
           // Stage the checkpoint file too
-          run(`git add "${checkpointFile}"`);
-          const result = run(`${addCmd} && git commit -m "${commitMsg.replace(/"/g, '\\"')}" 2>&1`);
-          if (result.includes("commit failed") || result.includes("nothing to commit")) {
+          run(["add", checkpointFile]);
+          // Stage based on mode
+          if (mode === "all") {
+            run(["add", "-A"]);
+          } else if (mode === "tracked") {
+            run(["add", "-u"]);
+          }
+          // mode === "staged": already staged, nothing extra to do
+          const result = run(["commit", "-m", commitMsg]);
+          if (result.includes("commit failed") || result.includes("nothing to commit") || result.startsWith("[command failed")) {
             // Rollback: unstage if commit failed
-            run("git reset HEAD 2>/dev/null");
+            run(["reset", "HEAD"]);
             commitResult = `commit failed: ${result}`;
           } else {
             commitResult = result;

src/tools/clarify-intent.ts

@@ -4,10 +4,31 @@ import { run, getBranch, getStatus, getRecentCommits, getDiffFiles, getStagedFil
 import { findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js";
 import { searchSemantic } from "../lib/timeline-db.js";
 import { getRelatedProjects } from "../lib/config.js";
-import { existsSync, readFileSync } from "fs";
+import { existsSync, readFileSync, readdirSync, statSync } from "fs";
+import { execFileSync } from "child_process";
 import { join, basename, resolve } from "path";
 import { loadAllContracts, searchContracts, formatContracts } from "../lib/contracts.js";
 
+/** Recursively find test files using Node.js fs */
+function findTestFiles(dir: string, maxDepth: number, limit: number, depth = 0): string[] {
+  const results: string[] = [];
+  if (depth > maxDepth || results.length >= limit) return results;
+  try {
+    const entries = readdirSync(dir, { withFileTypes: true });
+    for (const entry of entries) {
+      if (results.length >= limit) break;
+      const fullPath = join(dir, entry.name);
+      if (entry.isDirectory() && !entry.name.startsWith(".") && entry.name !== "node_modules") {
+        results.push(...findTestFiles(fullPath, maxDepth, limit - results.length, depth + 1));
+      } else if (entry.isFile() && /\.spec\.ts$/.test(entry.name)) {
+        // Return relative to PROJECT_DIR
+        results.push(fullPath.replace(PROJECT_DIR + "/", ""));
+      }
+    }
+  } catch { /* directory may not exist */ }
+  return results;
+}
+
 /** Parse test failures from common report formats without fragile shell pipelines */
 function getTestFailures(): string {
   // Try playwright JSON report
@@ -152,10 +173,24 @@ export function registerClarifyIntent(server: McpServer): void {
       let hasTestFailures = false;
 
       if (!area || area.includes("test") || area.includes("fix") || area.includes("ui") || area.includes("api")) {
-        const typeErrors = run("pnpm tsc --noEmit 2>&1 | grep -c 'error TS' || echo '0'");
-        hasTypeErrors = parseInt(typeErrors, 10) > 0;
+        let typeErrorCount = 0;
+        try {
+          execFileSync("pnpm", ["tsc", "--noEmit"], {
+            cwd: PROJECT_DIR,
+            encoding: "utf-8",
+            timeout: 30000,
+            stdio: ["pipe", "pipe", "pipe"],
+          });
+        } catch (e: any) {
+          const output = (e.stdout || "") + (e.stderr || "");
+          const matches = output.match(/error TS/g);
+          typeErrorCount = matches ? matches.length : 0;
+        }
+        const typeErrors = String(typeErrorCount);
+        hasTypeErrors = typeErrorCount > 0;
 
-        const testFiles = run("find tests -name '*.spec.ts' -maxdepth 4 2>/dev/null | head -20");
+        // Find test files using Node.js fs instead of shell find
+        const testFiles = findTestFiles(join(PROJECT_DIR, "tests"), 4, 20).join("\n");
         const failingTests = getTestFailures();
         hasTestFailures = failingTests !== "all passing" && failingTests !== "no test report found";
 

src/tools/enrich-agent-task.ts

@@ -8,11 +8,6 @@ import { execFileSync } from "child_process";
 import { join, basename } from "path";
 import { createHash } from "crypto";
 
-/** Sanitize user input for safe use in shell commands */
-function shellEscape(s: string): string {
-  return s.replace(/[^a-zA-Z0-9_\-./]/g, "");
-}
-
 /** Detect package manager from lockfiles */
 function detectPackageManager(): string {
   if (existsSync(join(PROJECT_DIR, "pnpm-lock.yaml"))) return "pnpm";
@@ -25,35 +20,57 @@ function detectPackageManager(): string {
 function findAreaFiles(area: string): string {
   if (!area) return getDiffFiles("HEAD~3");
 
-  const safeArea = shellEscape(area);
+  // Get all tracked files and filter in JS
+  const allFiles = run(["ls-files"]);
+  if (allFiles.startsWith("[")) return getDiffFiles("HEAD~3");
+
+  const fileList = allFiles.split("\n").filter(Boolean);
+  const areaLower = area.toLowerCase();
 
-  // If area looks like a path, search directly
+  let matches: string[];
   if (area.includes("/")) {
-    return run(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`);
+    // If area looks like a path, match prefix
+    matches = fileList.filter(f => f.startsWith(area));
+  } else {
+    // Search for area keyword in file paths
+    matches = fileList.filter(f => f.toLowerCase().includes(areaLower));
   }
 
-  // Search for area keyword in git-tracked file paths
-  const files = run(`git ls-files 2>/dev/null | grep -i '${safeArea}' | head -20`);
-  if (files && !files.startsWith("[command failed")) return files;
+  if (matches.length > 0) return matches.slice(0, 20).join("\n");
 
   // Fallback to recently changed files
   return getDiffFiles("HEAD~3");
 }
 
 /** Find related test files for an area */
 function findRelatedTests(area: string): string {
-  if (!area) return run("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10");
+  const allFiles = run(["ls-files"]);
+  if (allFiles.startsWith("[")) return "";
+
+  const testPattern = /\.(spec|test)\.(ts|tsx|js|jsx)$/;
+  const testFiles = allFiles.split("\n").filter(f => testPattern.test(f));
+
+  if (!area) return testFiles.slice(0, 10).join("\n");
 
-  const safeArea = shellEscape(area.split(/\s+/)[0]);
-  const tests = run(`git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | grep -i '${safeArea}' | head -10`);
-  return tests || run("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10");
+  const areaKeyword = area.split(/\s+/)[0].toLowerCase();
+  const areaTests = testFiles.filter(f => f.toLowerCase().includes(areaKeyword));
+  if (areaTests.length > 0) return areaTests.slice(0, 10).join("\n");
+
+  return testFiles.slice(0, 10).join("\n");
 }
 
 /** Get an example pattern from the first matching file */
 function getExamplePattern(files: string): string {
   const firstFile = files.split("\n").filter(Boolean)[0];
   if (!firstFile) return "no pattern available";
-  return run(`head -30 '${shellEscape(firstFile)}' 2>/dev/null || echo 'could not read file'`);
+  try {
+    const fullPath = join(PROJECT_DIR, firstFile);
+    const content = readFileSync(fullPath, "utf-8");
+    const lines = content.split("\n").slice(0, 30);
+    return lines.join("\n");
+  } catch {
+    return "could not read file";
+  }
 }
 
 // ---------------------------------------------------------------------------

src/tools/sequence-tasks.ts

@@ -90,7 +90,8 @@ export function registerSequenceTasks(server: McpServer): void {
       // For locality: infer directories from path-like tokens in task text
       if (strategy === "locality") {
         // Use git ls-files with a depth limit instead of find for performance
-        const gitFiles = run("git ls-files 2>/dev/null | head -1000");
+        const gitFilesRaw = run(["ls-files"]);
+        const gitFiles = gitFilesRaw.startsWith("[") ? "" : gitFilesRaw.split("\n").slice(0, 1000).join("\n");
         const knownDirs = new Set<string>();
         for (const f of gitFiles.split("\n").filter(Boolean)) {
           const parts = f.split("/");

src/tools/session-handoff.ts

@@ -2,14 +2,19 @@ import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { existsSync, readFileSync } from "fs";
 import { join } from "path";
+import { execFileSync } from "child_process";
 import { run, getBranch, getRecentCommits, getStatus } from "../lib/git.js";
 import { readIfExists, findWorkspaceDocs } from "../lib/files.js";
 import { STATE_DIR, now } from "../lib/state.js";
 
 /** Check if a CLI tool is available */
 function hasCommand(cmd: string): boolean {
-  const result = run(`command -v ${cmd} 2>/dev/null`);
-  return !!result && !result.startsWith("[command failed");
+  try {
+    execFileSync("which", [cmd], { encoding: "utf-8", stdio: ["pipe", "pipe", "pipe"] });
+    return true;
+  } catch {
+    return false;
+  }
 }
 
 export function registerSessionHandoff(server: McpServer): void {
@@ -44,7 +49,14 @@ export function registerSessionHandoff(server: McpServer): void {
 
         // Only try gh if it exists
         if (hasCommand("gh")) {
-          const openPRs = run("gh pr list --state open --json number,title,headRefName 2>/dev/null || echo '[]'");
+          let openPRs = "[]";
+          try {
+            openPRs = execFileSync("gh", ["pr", "list", "--state", "open", "--json", "number,title,headRefName"], {
+              encoding: "utf-8",
+              timeout: 10000,
+              stdio: ["pipe", "pipe", "pipe"],
+            }).trim();
+          } catch { /* gh not available or failed */ }
           if (openPRs && openPRs !== "[]") {
             sections.push(`## Open PRs\n\`\`\`json\n${openPRs}\n\`\`\``);
           }

src/tools/sharpen-followup.ts

@@ -27,15 +27,15 @@ function parsePortelainFiles(output: string): string[] {
 /** Get recently changed files, safe for first commit / shallow clones */
 function getRecentChangedFiles(): string[] {
   // Try HEAD~1..HEAD, fall back to just staged, then unstaged
-  const commands = [
-    "git diff --name-only HEAD~1 HEAD 2>/dev/null",
-    "git diff --name-only --cached 2>/dev/null",
-    "git diff --name-only 2>/dev/null",
+  const commands: string[][] = [
+    ["diff", "--name-only", "HEAD~1", "HEAD"],
+    ["diff", "--name-only", "--cached"],
+    ["diff", "--name-only"],
   ];
   const results = new Set<string>();
-  for (const cmd of commands) {
-    const out = run(cmd);
-    if (out) out.split("\n").filter(Boolean).forEach((f) => results.add(f));
+  for (const args of commands) {
+    const out = run(args);
+    if (out && !out.startsWith("[")) out.split("\n").filter(Boolean).forEach((f) => results.add(f));
     if (results.size > 0) break; // first successful source is enough
   }
   return [...results];
@@ -87,7 +87,7 @@ export function registerSharpenFollowup(server: McpServer): void {
       // Gather context to resolve ambiguity
       const contextFiles: string[] = [...(previous_files ?? [])];
       const recentChanged = getRecentChangedFiles();
-      const porcelainOutput = run("git status --porcelain 2>/dev/null");
+      const porcelainOutput = run(["status", "--porcelain"]);
       const untrackedOrModified = parsePortelainFiles(porcelainOutput);
 
       const allKnownFiles = [...new Set([...contextFiles, ...recentChanged, ...untrackedOrModified])].filter(Boolean);