fix: replace shell syntax in git.run() calls across 8 tools

src/lib/git.ts

@@ -1,4 +1,4 @@
-import { execFileSync } from "child_process";
+import { execFileSync, execSync } from "child_process";
 import { PROJECT_DIR } from "./files.js";
 import type { RunError } from "../types.js";
 
@@ -35,6 +35,29 @@ function gitCmd(cmdStr: string, opts?: { timeout?: number }): string {
   return run(cmdStr.split(/\s+/), opts);
 }
 
+/**
+ * Run an arbitrary shell command (with shell interpretation).
+ * Use only for non-git commands that need pipes, redirects, etc.
+ * For git commands, always prefer run() with array args.
+ */
+export function shell(cmd: string, opts: { timeout?: number } = {}): string {
+  try {
+    return execSync(cmd, {
+      cwd: PROJECT_DIR,
+      encoding: "utf-8",
+      timeout: opts.timeout || 10000,
+      maxBuffer: 1024 * 1024,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim();
+  } catch (e: any) {
+    const timedOut = e.killed === true || e.signal === "SIGTERM";
+    if (timedOut) return `[timed out after ${opts.timeout || 10000}ms]`;
+    const output = e.stdout?.trim() || e.stderr?.trim();
+    if (output) return output;
+    return `[command failed: ${cmd} (exit ${e.status ?? "?"})]`;
+  }
+}
+
 /** Get the current branch name. */
 export function getBranch(): string {
   return run(["branch", "--show-current"]);

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, statSync } 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 rawDiff = run(["diff", "--name-only", "HEAD~10"]);
+      const recentFiles = rawDiff.startsWith("[") ? [] : rawDiff.split("\n").filter(Boolean);
       const sections: string[] = [];
 
       // Doc freshness
@@ -75,7 +78,16 @@ 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 = (() => {
+          try {
+            const testDir = join(PROJECT_DIR, "tests");
+            const st = statSync(testDir);
+            if (!st.isDirectory()) return 0;
+            // Count test files using git ls-files for accuracy
+            const files = run(["ls-files", "tests/"]);
+            return files.split("\n").filter(f => /\.(spec|test)\.(ts|js)$/.test(f)).length;
+          } catch { return 0; }
+        })();
         sections.push(`## Tracking Docs\n${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

@@ -29,31 +29,50 @@ function findAreaFiles(area: string): string {
 
   // If area looks like a path, search directly
   if (area.includes("/")) {
-    return run(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`);
+    const result = run(["ls-files", "--", `${safeArea}*`]);
+    if (result && !result.startsWith("[")) {
+      return result.split("\n").slice(0, 20).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 allFiles = run(["ls-files"]);
+  if (allFiles && !allFiles.startsWith("[")) {
+    const matched = allFiles.split("\n")
+      .filter(f => f.toLowerCase().includes(safeArea.toLowerCase()))
+      .slice(0, 20);
+    if (matched.length > 0) return matched.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)$' | head -10");
+  const allFiles = run(["ls-files"]);
+  if (!allFiles || allFiles.startsWith("[")) return "";
+
+  const testFiles = allFiles.split("\n")
+    .filter(f => /\.(spec|test)\.(ts|tsx|js|jsx)$/.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 safeArea = shellEscape(area.split(/\s+/)[0]).toLowerCase();
+  const areaTests = testFiles.filter(f => f.toLowerCase().includes(safeArea)).slice(0, 10);
+  return areaTests.length > 0 ? areaTests.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

@@ -128,7 +128,11 @@ export function registerScopeWork(server: McpServer): void {
         .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"]);
+        matchedFiles = allFiles.split("\n")
+          .filter(f => new RegExp(grepTerms.join("|"), "i").test(f))
+          .slice(0, 30)
+          .join("\n");
       }
 
       // Check which relevant dirs actually exist (with path traversal protection)

src/tools/sequence-tasks.ts

@@ -90,7 +90,8 @@ 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

@@ -2,13 +2,13 @@ import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { existsSync, readFileSync } from "fs";
 import { join } from "path";
-import { run, getBranch, getRecentCommits, getStatus } from "../lib/git.js";
+import { run, shell, 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`);
+  const result = shell(`command -v ${cmd} 2>/dev/null`);
   return !!result && !result.startsWith("[command failed");
 }
 
@@ -44,7 +44,7 @@ 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 '[]'");
+          const openPRs = shell("gh pr list --state open --json number,title,headRefName 2>/dev/null || echo '[]'");
           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);

src/tools/token-audit.ts

@@ -1,7 +1,7 @@
 // CATEGORY 5: token_audit — Token Efficiency
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { run } from "../lib/git.js";
+import { run, shell } 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";
@@ -39,8 +39,8 @@ 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 +62,11 @@ 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 < '${shellEscape(f)}' 2>/dev/null`);
-        const lines = parseInt(wc) || 0;
+        let lines = 0;
+        try {
+          const content = readFileSync(join(PROJECT_DIR, f), "utf-8");
+          lines = content.split("\n").length;
+        } catch { /* skip unreadable files */ }
         estimatedContextTokens += lines * AVG_LINE_BYTES * AVG_TOKENS_PER_BYTE;
         if (lines > 500) {
           largeFiles.push(`${f} (${lines} lines)`);
@@ -80,8 +82,8 @@ export function registerTokenAudit(server: McpServer): void {
       // 3. CLAUDE.md bloat check
       const claudeMd = readIfExists("CLAUDE.md", 1);
       if (claudeMd !== null) {
-        const stat = run(`wc -c < '${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 +141,7 @@ 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)}'`);
+              : shell(`tail -c ${MAX_TOOL_LOG_BYTES} '${shellEscape(toolLogPath)}'`);
 
             const lines = raw.trim().split("\n").filter(Boolean);
             totalToolCalls = lines.length;

src/tools/verify-completion.ts

@@ -1,8 +1,8 @@
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { run, getStatus } from "../lib/git.js";
+import { run, shell, getStatus } from "../lib/git.js";
 import { PROJECT_DIR } from "../lib/files.js";
-import { existsSync } from "fs";
+import { existsSync, readFileSync } from "fs";
 import { join } from "path";
 
 /** Detect package manager from lockfiles */
@@ -34,7 +34,9 @@ function detectTestRunner(): string | null {
 /** 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 pkgPath = join(PROJECT_DIR, "package.json");
+    if (!existsSync(pkgPath)) return false;
+    const pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
     return !!pkg?.scripts?.build;
   } catch { return false; }
 }
@@ -55,7 +57,7 @@ export function registerVerifyCompletion(server: McpServer): void {
       const checks: { name: string; passed: boolean; detail: string }[] = [];
 
       // 1. Type check (single invocation, extract both result and count)
-      const tscOutput = run(`${pm === "npx" ? "npx" : pm} tsc --noEmit 2>&1 | tail -20`);
+      const tscOutput = shell(`${pm === "npx" ? "npx" : pm} tsc --noEmit 2>&1 | tail -20`);
       const errorLines = tscOutput.split("\n").filter(l => /error TS\d+/.test(l));
       const typePassed = errorLines.length === 0;
       checks.push({
@@ -80,7 +82,7 @@ export function registerVerifyCompletion(server: McpServer): void {
       // 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 = "";
 
         if (runner === "playwright") {
@@ -112,7 +114,7 @@ export function registerVerifyCompletion(server: McpServer): void {
         }
 
         if (testCmd) {
-          const testResult = run(testCmd, { timeout: 120000 });
+          const testResult = shell(testCmd, { timeout: 120000 });
           const testPassed = /pass/i.test(testResult) && !/fail/i.test(testResult);
           checks.push({
             name: "Tests",
@@ -130,7 +132,7 @@ export function registerVerifyCompletion(server: McpServer): void {
 
       // 4. Build check (only if build script exists and not skipped)
       if (!skip_build && hasBuildScript()) {
-        const buildCheck = run(`${pm === "npx" ? "npm run" : pm} build 2>&1 | tail -10`, { timeout: 60000 });
+        const buildCheck = shell(`${pm === "npx" ? "npm run" : pm} build 2>&1 | tail -10`, { timeout: 60000 });
         const buildPassed = !/\b[Ee]rror\b/.test(buildCheck) || /Successfully compiled/.test(buildCheck);
         checks.push({
           name: "Build",