fix: replace shell syntax in run() calls with proper APIs

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 +35,52 @@ function gitCmd(cmdStr: string, opts?: { timeout?: number }): string {
   return run(cmdStr.split(/\s+/), opts);
 }
 
+/**
+ * Run an arbitrary shell command (with shell: true).
+ * Use this for non-git commands or commands requiring pipes/redirects.
+ * Callers are responsible for sanitizing any interpolated values.
+ */
+export function shell(cmd: string, opts: { timeout?: number; cwd?: string } = {}): string {
+  try {
+    return execSync(cmd, {
+      cwd: opts.cwd || PROJECT_DIR,
+      encoding: "utf-8",
+      timeout: opts.timeout || 10000,
+      maxBuffer: 1024 * 1024,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim();
+  } catch (e: any) {
+    if (e.killed === true || e.signal === "SIGTERM") {
+      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 ${e.status ?? "?"})]`;
+  }
+}
+
+/**
+ * Get git-tracked files, optionally filtered. Uses execFileSync (no shell).
+ * Replaces patterns like: run("git ls-files | grep ... | head ...")
+ */
+export function getTrackedFiles(opts: { pattern?: RegExp; limit?: number } = {}): string[] {
+  const raw = run(["ls-files"]);
+  if (raw.startsWith("[")) return [];
+  let files = raw.split("\n").filter(Boolean);
+  if (opts.pattern) files = files.filter(f => opts.pattern!.test(f));
+  if (opts.limit) files = files.slice(0, opts.limit);
+  return files;
+}
+
+/**
+ * Get git-tracked files matching a path prefix.
+ */
+export function getTrackedFilesInPath(prefix: string, limit = 20): string[] {
+  const result = run(["ls-files", "--", `${prefix}*`]);
+  if (result.startsWith("[")) return [];
+  return result.split("\n").filter(Boolean).slice(0, limit);
+}
+
 /** Get the current branch name. */
 export function getBranch(): string {
   return run(["branch", "--show-current"]);

src/tools/enrich-agent-task.ts

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { run, getDiffFiles } from "../lib/git.js";
+import { run, getDiffFiles, getTrackedFiles, getTrackedFilesInPath } from "../lib/git.js";
 import { PROJECT_DIR } from "../lib/files.js";
 import { getConfig, type RelatedProject } from "../lib/config.js";
 import { existsSync, readFileSync } from "fs";
@@ -25,35 +25,43 @@ function detectPackageManager(): string {
 function findAreaFiles(area: string): string {
   if (!area) return getDiffFiles("HEAD~3");
 
-  const safeArea = shellEscape(area);
-
   // If area looks like a path, search directly
   if (area.includes("/")) {
-    return run(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`);
+    return getTrackedFilesInPath(area, 20).join("\n") || getDiffFiles("HEAD~3");
   }
 
   // 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 safeArea = shellEscape(area);
+  const pattern = new RegExp(safeArea, "i");
+  const files = getTrackedFiles({ pattern, limit: 20 });
+  if (files.length > 0) return files.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)$' | head -10");
+  const testPattern = /\.(spec|test)\.(ts|tsx|js|jsx)$/;
+  const allTests = getTrackedFiles({ pattern: testPattern, limit: 100 });
+
+  if (!area) return allTests.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 = allTests.filter(f => f.toLowerCase().includes(safeArea)).slice(0, 10);
+  return (areaTests.length > 0 ? areaTests : allTests.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

@@ -1,7 +1,7 @@
 // CATEGORY 1: scope_work — Plans
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { run, getBranch, getRecentCommits, getStatus } from "../lib/git.js";
+import { run, getBranch, getRecentCommits, getStatus, getTrackedFiles } from "../lib/git.js";
 import { readIfExists, findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js";
 import { searchSemantic } from "../lib/timeline-db.js";
 import { getRelatedProjects } from "../lib/config.js";
@@ -127,8 +127,8 @@ 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 pattern = new RegExp(grepTerms.join("|"), "i");
+        matchedFiles = getTrackedFiles({ pattern, limit: 30 }).join("\n");
       }
 
       // Check which relevant dirs actually exist (with path traversal protection)

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, getBranch, getRecentCommits, getStatus, shell } 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/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 +57,11 @@ 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} (${lines} lines)`);
@@ -80,8 +77,8 @@ export function registerTokenAudit(server: McpServer): void {
       // 3. CLAUDE.md bloat check
       const claudeMd = readIfExists("CLAUDE.md", 1);
       if (claudeMd !== null) {
-        const stat = run(`wc -c < '${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");
@@ -137,9 +134,16 @@ 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)}'`);
+            let raw: string;
+            if (stat.size <= MAX_TOOL_LOG_BYTES) {
+              raw = readFileSync(toolLogPath, "utf-8");
+            } else {
+              const fd = openSync(toolLogPath, "r");
+              const buf = Buffer.alloc(MAX_TOOL_LOG_BYTES);
+              readSync(fd, buf, 0, MAX_TOOL_LOG_BYTES, stat.size - MAX_TOOL_LOG_BYTES);
+              closeSync(fd);
+              raw = buf.toString("utf-8");
+            }
 
             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, getStatus, shell } 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 +34,8 @@ 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 raw = readFileSync(join(PROJECT_DIR, "package.json"), "utf-8");
+    const pkg = JSON.parse(raw);
     return !!pkg?.scripts?.build;
   } catch { return false; }
 }
@@ -55,7 +56,7 @@ 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 +81,7 @@ 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 +113,7 @@ 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 +131,7 @@ 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",