fix: replace run() with shell() across 9 tools — closes #215

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";
 
@@ -30,6 +30,29 @@ export function run(argsOrCmd: string | string[], opts: { timeout?: number } = {
   }
 }
 
+/**
+ * Run an arbitrary shell command string (supports pipes, redirects, etc.).
+ * Use for non-git commands or when shell features are needed.
+ * Returns stdout on success, descriptive error string on failure.
+ */
+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 ?? "?"})]`;
+  }
+}
+
 /** Convenience: run a raw command string (split on spaces). Only for simple, known-safe commands. */
 function gitCmd(cmdStr: string, opts?: { timeout?: number }): string {
   return run(cmdStr.split(/\s+/), opts);

src/tools/audit-workspace.ts

@@ -1,5 +1,5 @@
 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 } from "../lib/files.js";
 
 /** Extract top-level work areas from file paths generically */
@@ -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 = shell("git diff --name-only HEAD~10 2>/dev/null || echo ''").split("\n").filter(Boolean);
       const sections: string[] = [];
 
       // Doc freshness
@@ -75,7 +75,7 @@ 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 = parseInt(shell("find tests -name '*.spec.ts' -o -name '*.test.ts' 2>/dev/null | wc -l").trim()) || 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/checkpoint.ts

@@ -2,7 +2,7 @@ import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { writeFileSync, existsSync, mkdirSync } from "fs";
 import { join, dirname } from "path";
-import { run, getBranch, getStatus, getLastCommit, getStagedFiles } from "../lib/git.js";
+import { run, shell, getBranch, getStatus, getLastCommit, getStagedFiles } from "../lib/git.js";
 import { PROJECT_DIR } from "../lib/files.js";
 import { appendLog, now } from "../lib/state.js";
 
@@ -84,11 +84,11 @@ ${dirty || "clean"}
 
         if (commitResult === "no uncommitted changes") {
           // Stage the checkpoint file too
-          run(`git add "${checkpointFile}"`);
-          const result = run(`${addCmd} && git commit -m "${commitMsg.replace(/"/g, '\\"')}" 2>&1`);
+          run(["add", checkpointFile]);
+          const result = shell(`${addCmd} && git commit -m "${commitMsg.replace(/"/g, '\\"')}" 2>&1`);
           if (result.includes("commit failed") || result.includes("nothing to commit")) {
             // 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

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { run, getBranch, getStatus, getRecentCommits, getDiffFiles, getStagedFiles } from "../lib/git.js";
+import { run, shell, getBranch, getStatus, getRecentCommits, getDiffFiles, getStagedFiles } from "../lib/git.js";
 import { findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js";
 import { searchSemantic } from "../lib/timeline-db.js";
 import { getRelatedProjects } from "../lib/config.js";
@@ -152,10 +152,10 @@ 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'");
+        const typeErrors = shell("pnpm tsc --noEmit 2>&1 | grep -c 'error TS' || echo '0'");
         hasTypeErrors = parseInt(typeErrors, 10) > 0;
 
-        const testFiles = run("find tests -name '*.spec.ts' -maxdepth 4 2>/dev/null | head -20");
+        const testFiles = shell("find tests -name '*.spec.ts' -maxdepth 4 2>/dev/null | head -20");
         const failingTests = getTestFailures();
         hasTestFailures = failingTests !== "all passing" && failingTests !== "no test report found";
 

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, shell, getDiffFiles } from "../lib/git.js";
 import { PROJECT_DIR } from "../lib/files.js";
 import { getConfig, type RelatedProject } from "../lib/config.js";
 import { existsSync, readFileSync } from "fs";
@@ -29,11 +29,11 @@ function findAreaFiles(area: string): string {
 
   // If area looks like a path, search directly
   if (area.includes("/")) {
-    return run(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`);
+    return shell(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`);
   }
 
   // Search for area keyword in git-tracked file paths
-  const files = run(`git ls-files 2>/dev/null | grep -i '${safeArea}' | head -20`);
+  const files = shell(`git ls-files 2>/dev/null | grep -i '${safeArea}' | head -20`);
   if (files && !files.startsWith("[command failed")) return files;
 
   // Fallback to recently changed files
@@ -42,18 +42,18 @@ function findAreaFiles(area: string): string {
 
 /** 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)$' | head -10");
+  if (!area) return shell("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10");
 
   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)$' | head -10");
+  const tests = shell(`git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | grep -i '${safeArea}' | head -10`);
+  return tests || shell("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10");
 }
 
 /** 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 '${shellEscape(firstFile)}' 2>/dev/null || echo 'could not read file'`);
+  return shell(`head -30 '${shellEscape(firstFile)}' 2>/dev/null || echo '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, shell, getBranch, getRecentCommits, getStatus } 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";
@@ -128,7 +128,7 @@ 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 '${pattern}' | head -30`);
+        matchedFiles = shell(`git ls-files | head -500 | grep -iE '${pattern}' | head -30`);
       }
 
       // Check which relevant dirs actually exist (with path traversal protection)

src/tools/sequence-tasks.ts

@@ -1,7 +1,7 @@
 // CATEGORY 6: sequence_tasks — Sequencing
 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 { now } from "../lib/state.js";
 import { PROJECT_DIR } from "../lib/files.js";
 import { existsSync } from "fs";
@@ -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 = shell("git ls-files 2>/dev/null | head -1000");
         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

@@ -1,7 +1,7 @@
 // CATEGORY 4: sharpen_followup — Follow-up Specificity
 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 { now } from "../lib/state.js";
 
 /** Parse git porcelain output into deduplicated file paths, handling renames (R/C) */
@@ -27,14 +27,14 @@ 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);
+  for (const args of commands) {
+    const out = run(args);
     if (out) out.split("\n").filter(Boolean).forEach((f) => results.add(f));
     if (results.size > 0) break; // first successful source is enough
   }
@@ -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/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 +34,8 @@ 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",