fix(#302): remove shell syntax from run() calls in 4 tools

src/tools/checkpoint.ts

@@ -84,11 +84,17 @@ ${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`);
-          if (result.includes("commit failed") || result.includes("nothing to commit")) {
+          run(["add", checkpointFile]);
+          // Stage files based on mode
+          if (mode === "tracked") {
+            run(["add", "-u"]);
+          } else if (mode === "all") {
+            run(["add", "-A"]);
+          }
+          const result = run(["commit", "-m", commitMsg]);
+          if (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/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 allGitFiles = run(["ls-files"]);
+        const gitFiles = allGitFiles.startsWith("[") ? "" : allGitFiles.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

@@ -5,11 +5,16 @@ 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";
+import { execFileSync } from "child_process";
 
 /** 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 {
@@ -44,9 +49,17 @@ 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 '[]'");
-          if (openPRs && openPRs !== "[]") {
-            sections.push(`## Open PRs\n\`\`\`json\n${openPRs}\n\`\`\``);
+          try {
+            const openPRs = execFileSync("gh", ["pr", "list", "--state", "open", "--json", "number,title,headRefName"], {
+              encoding: "utf-8",
+              timeout: 10000,
+              stdio: ["pipe", "pipe", "pipe"],
+            }).trim();
+            if (openPRs && openPRs !== "[]") {
+              sections.push(`## Open PRs\n\`\`\`json\n${openPRs}\n\`\`\``);
+            }
+          } catch {
+            // gh pr list failed, skip
           }
         }
 

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, getDiffFiles, getStagedFiles } from "../lib/git.js";
 import { now } from "../lib/state.js";
 
 /** Parse git porcelain output into deduplicated file paths, handling renames (R/C) */
@@ -26,19 +26,24 @@ 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 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));
-    if (results.size > 0) break; // first successful source is enough
+  // Try HEAD~1..HEAD first
+  const committed = run(["diff", "--name-only", "HEAD~1", "HEAD"]);
+  if (committed && !committed.startsWith("[")) {
+    const files = committed.split("\n").filter(Boolean);
+    if (files.length > 0) return files;
   }
-  return [...results];
+  // Fall back to staged
+  const staged = getStagedFiles();
+  if (staged && !staged.startsWith("[")) {
+    const files = staged.split("\n").filter(Boolean);
+    if (files.length > 0) return files;
+  }
+  // Fall back to unstaged
+  const unstaged = run(["diff", "--name-only"]);
+  if (unstaged && !unstaged.startsWith("[")) {
+    return unstaged.split("\n").filter(Boolean);
+  }
+  return [];
 }
 
 export function registerSharpenFollowup(server: McpServer): void {
@@ -87,7 +92,7 @@ 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/what-changed.ts

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { run, getBranch, getDiffStat } from "../lib/git.js";
+import { run, getBranch, getDiffFiles, getDiffStat } from "../lib/git.js";
 
 export function registerWhatChanged(server: McpServer): void {
   server.tool(
@@ -12,8 +12,9 @@ export function registerWhatChanged(server: McpServer): void {
     async ({ since }) => {
       const ref = since || "HEAD~5";
       const diffStat = getDiffStat(ref);
-      const diffFiles = run(`git diff ${ref} --name-only 2>/dev/null || git diff HEAD~3 --name-only`);
-      const log = run(`git log ${ref}..HEAD --oneline 2>/dev/null || git log -5 --oneline`);
+      const diffFiles = getDiffFiles(ref);
+      const logResult = run(["log", `${ref}..HEAD`, "--oneline"]);
+      const log = logResult.startsWith("[") ? run(["log", "-5", "--oneline"]) : logResult;
       const branch = getBranch();
 
       const fileList = diffFiles.split("\n").filter(Boolean);