fix: replace shell syntax in run() calls across all 8 remaining tools

src/tools/audit-workspace.ts

@@ -36,7 +36,7 @@ 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 recentFiles = run(["diff", "--name-only", "HEAD~10"]).split("\n").filter(Boolean);
       const sections: string[] = [];
 
       // Doc freshness
@@ -75,7 +75,10 @@ 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;
+        const testFilesCount = run(["ls-files", "tests/"])
+          .split("\n")
+          .filter(f => /\.(spec|test)\.(ts|tsx|js|jsx)$/.test(f))
+          .length;
         sections.push(`## Tracking Docs\n${trackingDocs.map(([n]) => {
           const age = docStatus.find(d => d.name === n)?.ageHours ?? "?";
           return `- .claude/${n} — last updated ${age}h ago`;

src/tools/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 +20,46 @@ function detectPackageManager(): string {
 function findAreaFiles(area: string): string {
   if (!area) return getDiffFiles("HEAD~3");
 
-  const safeArea = shellEscape(area);
+  const allFiles = run(["ls-files"]).split("\n").filter(Boolean);
 
   // If area looks like a path, search directly
   if (area.includes("/")) {
-    return run(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`);
+    const matches = allFiles.filter(f => f.startsWith(area)).slice(0, 20);
+    if (matches.length > 0) return matches.join("\n");
   }
 
   // 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;
+  const pattern = new RegExp(area.replace(/[^a-zA-Z0-9_\-./]/g, ""), "i");
+  const matches = allFiles.filter(f => pattern.test(f)).slice(0, 20);
+  if (matches.length > 0) return matches.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)$' | head -10");
+  const allFiles = run(["ls-files"]).split("\n").filter(Boolean);
+  const testFiles = allFiles.filter(f => /\.(spec|test)\.(ts|tsx|js|jsx)$/.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 keyword = area.split(/\s+/)[0].replace(/[^a-zA-Z0-9_\-./]/g, "");
+  const pattern = new RegExp(keyword, "i");
+  const matched = testFiles.filter(f => pattern.test(f)).slice(0, 10);
+  return matched.length > 0 ? matched.join("\n") : 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 content = readFileSync(join(PROJECT_DIR, firstFile), "utf-8");
+    return content.split("\n").slice(0, 30).join("\n");
+  } catch {
+    return "could not read file";
+  }
 }
 
 // ---------------------------------------------------------------------------

src/tools/scope-work.ts

@@ -17,11 +17,6 @@ const STOP_WORDS = new Set([
   "like", "some", "each", "only", "need", "want", "please", "update", "change",
 ]);
 
-/** Shell-escape a string for use inside single quotes */
-function shellEscape(s: string): string {
-  return s.replace(/'/g, "'\\''");
-}
-
 /** Safely parse git porcelain status lines */
 function parsePortelainFiles(porcelain: string): string[] {
   if (!porcelain.trim()) return [];
@@ -93,9 +88,9 @@ export function registerScopeWork(server: McpServer): void {
       const timestamp = now();
       const currentBranch = branch ?? getBranch();
       const recentCommits = getRecentCommits(10);
-      const porcelain = run("git status --porcelain");
+      const porcelain = run(["status", "--porcelain"]);
       const dirtyFiles = parsePortelainFiles(porcelain);
-      const diffStat = dirtyFiles.length > 0 ? run("git diff --stat") : "(clean working tree)";
+      const diffStat = dirtyFiles.length > 0 ? run(["diff", "--stat"]) : "(clean working tree)";
 
       // Scan for relevant files based on task keywords
       const keywords = task.toLowerCase().split(/\s+/);
@@ -127,8 +122,10 @@ export function registerScopeWork(server: McpServer): void {
         .filter((k) => k.length > 2)
         .slice(0, 5);
       if (grepTerms.length > 0) {
-        const pattern = shellEscape(grepTerms.join("|"));
-        matchedFiles = run(`git ls-files | head -500 | grep -iE '${pattern}' | head -30`);
+        const allFiles = run(["ls-files"]);
+        const fileLines = allFiles.split("\n").filter(Boolean).slice(0, 500);
+        const pattern = new RegExp(grepTerms.join("|"), "i");
+        matchedFiles = fileLines.filter(f => pattern.test(f)).slice(0, 30).join("\n");
       }
 
       // Check which relevant dirs actually exist (with path traversal protection)

src/tools/sequence-tasks.ts

@@ -90,7 +90,7 @@ 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 gitFiles = run(["ls-files"]).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

@@ -1,15 +1,20 @@
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { existsSync, readFileSync } from "fs";
+import { execFileSync } from "child_process";
 import { join } from "path";
 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"], timeout: 3000 });
+    return true;
+  } catch {
+    return false;
+  }
 }
 
 export function registerSessionHandoff(server: McpServer): void {
@@ -44,7 +49,15 @@ 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"], {
+              cwd: process.cwd(),
+              encoding: "utf-8",
+              timeout: 10000,
+              stdio: ["pipe", "pipe", "pipe"],
+            }).trim();
+          } catch { /* gh not available or not in a repo */ }
           if (openPRs && openPRs !== "[]") {
             sections.push(`## Open PRs\n\`\`\`json\n${openPRs}\n\`\`\``);
           }

src/tools/sharpen-followup.ts

@@ -27,10 +27,10 @@ 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) {
@@ -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);

src/tools/token-audit.ts

@@ -4,14 +4,9 @@ import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { run } from "../lib/git.js";
 import { readIfExists, findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js";
 import { loadState, saveState, now, STATE_DIR } from "../lib/state.js";
-import { readFileSync, existsSync, statSync } from "fs";
+import { readFileSync, existsSync, statSync, openSync, readSync, closeSync } from "fs";
 import { join } from "path";
 
-/** Shell-escape a filename for safe interpolation */
-function shellEscape(s: string): string {
-  return s.replace(/'/g, "'\\''");
-}
-
 /**
  * Grade thresholds rationale:
  * - A (0-10):  Minimal waste — small diffs, targeted reads, lean context
@@ -39,8 +34,8 @@ export function registerTokenAudit(server: McpServer): void {
       let wasteScore = 0;
 
       // 1. Git diff size & dirty file count
-      const diffStat = run("git diff --stat --no-color 2>/dev/null");
-      const dirtyFiles = run("git diff --name-only 2>/dev/null");
+      const diffStat = run(["diff", "--stat", "--no-color"]);
+      const dirtyFiles = run(["diff", "--name-only"]);
       const dirtyList = dirtyFiles.split("\n").filter(Boolean);
       const dirtyCount = dirtyList.length;
 
@@ -62,9 +57,12 @@ export function registerTokenAudit(server: McpServer): void {
       const largeFiles: string[] = [];
 
       for (const f of dirtyList.slice(0, 30)) {
-        // Use shell-safe quoting instead of interpolation
-        const wc = run(`wc -l < '${shellEscape(f)}' 2>/dev/null`);
-        const lines = parseInt(wc) || 0;
+        // Count lines using Node.js fs instead of shell wc
+        let lines = 0;
+        try {
+          const content = readFileSync(join(PROJECT_DIR, f), "utf-8");
+          lines = content.split("\n").length;
+        } catch { /* skip unreadable files */ }
         estimatedContextTokens += lines * AVG_LINE_BYTES * AVG_TOKENS_PER_BYTE;
         if (lines > 500) {
           largeFiles.push(`${f} (${lines} lines)`);
@@ -80,8 +78,8 @@ export function registerTokenAudit(server: McpServer): void {
       // 3. CLAUDE.md bloat check
       const claudeMd = readIfExists("CLAUDE.md", 1);
       if (claudeMd !== null) {
-        const stat = run(`wc -c < '${shellEscape("CLAUDE.md")}' 2>/dev/null`);
-        const bytes = parseInt(stat) || 0;
+        let bytes = 0;
+        try { bytes = statSync(join(PROJECT_DIR, "CLAUDE.md")).size; } catch { /* ignore */ }
         if (bytes > 5120) {
           patterns.push(`CLAUDE.md is ${(bytes / 1024).toFixed(1)}KB — injected every session, burns tokens on paste`);
           recommendations.push("Trim CLAUDE.md to essentials (<5KB). Move reference docs to files read on-demand");
@@ -139,7 +137,13 @@ export function registerTokenAudit(server: McpServer): void {
             // Read with size cap: take the tail if too large
             const raw = stat.size <= MAX_TOOL_LOG_BYTES
               ? readFileSync(toolLogPath, "utf-8")
-              : run(`tail -c ${MAX_TOOL_LOG_BYTES} '${shellEscape(toolLogPath)}'`);
+              : (() => {
+                  const fd = openSync(toolLogPath, "r");
+                  const buf = Buffer.alloc(MAX_TOOL_LOG_BYTES);
+                  const bytesRead = readSync(fd, buf, 0, MAX_TOOL_LOG_BYTES, stat.size - MAX_TOOL_LOG_BYTES);
+                  closeSync(fd);
+                  return buf.subarray(0, bytesRead).toString("utf-8");
+                })();
 
             const lines = raw.trim().split("\n").filter(Boolean);
             totalToolCalls = lines.length;

src/tools/verify-completion.ts

@@ -2,9 +2,25 @@
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { run, getStatus } from "../lib/git.js";
 import { PROJECT_DIR } from "../lib/files.js";
-import { existsSync } from "fs";
+import { existsSync, readFileSync } from "fs";
+import { execFileSync } from "child_process";
 import { join } from "path";
 
+/** Run a non-git command safely, returning stdout or empty string on failure */
+function execSafe(cmd: string, args: string[], opts?: { timeout?: number }): string {
+  try {
+    return execFileSync(cmd, args, {
+      cwd: PROJECT_DIR,
+      encoding: "utf-8",
+      timeout: opts?.timeout || 30000,
+      maxBuffer: 1024 * 1024,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim();
+  } catch (e: any) {
+    return e.stdout?.trim?.() || "";
+  }
+}
+
 /** Detect package manager from lockfiles */
 function detectPM(): string {
   if (existsSync(join(PROJECT_DIR, "pnpm-lock.yaml"))) return "pnpm";
@@ -34,7 +50,8 @@
 /** Check if a build script exists in package.json */
 function hasBuildScript(): boolean {
   try {
-    const pkg = JSON.parse(run("cat package.json 2>/dev/null"));
+    const raw = readFileSync(join(PROJECT_DIR, "package.json"), "utf-8");
+    const pkg = JSON.parse(raw);
     return !!pkg?.scripts?.build;
   } catch { return false; }
 }
@@ -55,7 +72,9 @@
       const checks: { name: string; passed: boolean; detail: string }[] = [];
 
       // 1. Type check (single invocation, extract both result and count)
-      const tscOutput = run(`${pm === "npx" ? "npx" : pm} tsc --noEmit 2>&1 | tail -20`);
+      const tscCmd = pm === "npx" ? "npx" : pm;
+      const tscArgs = pm === "npx" ? ["tsc", "--noEmit"] : ["exec", "tsc", "--", "--noEmit"];
+      const tscOutput = execSafe(tscCmd, tscArgs, { timeout: 60000 });
       const errorLines = tscOutput.split("\n").filter(l => /error TS\d+/.test(l));
       const typePassed = errorLines.length === 0;
       checks.push({
@@ -80,39 +99,42 @@
       // 3. Tests
       if (!skip_tests) {
         const runner = detectTestRunner();
-        const changedFiles = run("git diff --name-only HEAD~1 2>/dev/null").split("\n").filter(Boolean);
+        const changedFiles = run(["diff", "--name-only", "HEAD~1"]).split("\n").filter(Boolean);
         let testCmd = "";
 
+        // Build test command as [cmd, ...args] for execSafe
+        let testArgs: { cmd: string; args: string[] } | null = null;
+
         if (runner === "playwright") {
-          const runnerCmd = `${pm === "npx" ? "npx" : `${pm} exec`} playwright test`;
+          const baseCmd = pm === "npx" ? "npx" : pm;
+          const baseArgs = pm === "npx" ? ["playwright", "test"] : ["exec", "playwright", "test"];
           if (test_scope && test_scope !== "all") {
-            testCmd = test_scope.endsWith(".spec.ts") || test_scope.endsWith(".test.ts")
-              ? `${runnerCmd} ${test_scope} --reporter=line 2>&1 | tail -20`
-              : `${runnerCmd} --grep "${test_scope}" --reporter=line 2>&1 | tail -20`;
+            testArgs = test_scope.endsWith(".spec.ts") || test_scope.endsWith(".test.ts")
+              ? { cmd: baseCmd, args: [...baseArgs, test_scope, "--reporter=line"] }
+              : { cmd: baseCmd, args: [...baseArgs, "--grep", test_scope, "--reporter=line"] };
           } else {
-            // Auto-detect from changed files
             const changedTests = changedFiles.filter(f => /\.(spec|test)\.(ts|tsx|js)$/.test(f)).slice(0, 5);
             if (changedTests.length > 0) {
-              testCmd = `${runnerCmd} ${changedTests.join(" ")} --reporter=line 2>&1 | tail -20`;
+              testArgs = { cmd: baseCmd, args: [...baseArgs, ...changedTests, "--reporter=line"] };
             }
           }
         } else if (runner === "vitest" || runner === "jest") {
-          const runnerCmd = `${pm === "npx" ? "npx" : `${pm} exec`} ${runner}`;
+          const baseCmd = pm === "npx" ? "npx" : pm;
+          const baseArgs = pm === "npx" ? [runner] : ["exec", runner, "--"];
           if (test_scope && test_scope !== "all") {
-            testCmd = `${runnerCmd} --run ${test_scope} 2>&1 | tail -20`;
+            testArgs = { cmd: baseCmd, args: [...baseArgs, "--run", test_scope] };
           } else {
             const changedTests = changedFiles.filter(f => /\.(spec|test)\.(ts|tsx|js)$/.test(f)).slice(0, 5);
             if (changedTests.length > 0) {
-              testCmd = `${runnerCmd} --run ${changedTests.join(" ")} 2>&1 | tail -20`;
+              testArgs = { cmd: baseCmd, args: [...baseArgs, "--run", ...changedTests] };
             }
           }
         } else if (test_scope) {
-          // No recognized runner but scope given — try npm test
-          testCmd = `${pm} test 2>&1 | tail -20`;
+          testArgs = { cmd: pm, args: ["test"] };
         }
 
-        if (testCmd) {
-          const testResult = run(testCmd, { timeout: 120000 });
+        if (testArgs) {
+          const testResult = execSafe(testArgs.cmd, testArgs.args, { timeout: 120000 });
           const testPassed = /pass/i.test(testResult) && !/fail/i.test(testResult);
           checks.push({
             name: "Tests",
@@ -130,7 +152,9 @@
 
       // 4. Build check (only if build script exists and not skipped)
       if (!skip_build && hasBuildScript()) {
-        const buildCheck = run(`${pm === "npx" ? "npm run" : pm} build 2>&1 | tail -10`, { timeout: 60000 });
+        const buildCmd = pm === "npx" ? "npm" : pm;
+        const buildArgs = pm === "npx" ? ["run", "build"] : ["run", "build"];
+        const buildCheck = execSafe(buildCmd, buildArgs, { timeout: 60000 });
         const buildPassed = !/\b[Ee]rror\b/.test(buildCheck) || /Successfully compiled/.test(buildCheck);
         checks.push({
           name: "Build",