fix: remove shell syntax from run() in checkpoint, sharpen-followup, sequence-tasks, session-handoff (#302)

src/tools/checkpoint.ts

@@ -63,32 +63,27 @@ ${dirty || "clean"}
         const shortSummary = summary.split("\n")[0].slice(0, 72);
         const commitMsg = `checkpoint: ${shortSummary}`;
 
-        let addCmd: string;
-        switch (mode) {
-          case "staged": {
-            const staged = getStagedFiles();
-            if (!staged) {
-              commitResult = "nothing staged — skipped commit (use 'tracked' or 'all' mode, or stage files first)";
-            }
-            addCmd = "true"; // noop, already staged
-            break;
+        if (mode === "staged") {
+          const staged = getStagedFiles();
+          if (!staged) {
+            commitResult = "nothing staged — skipped commit (use 'tracked' or 'all' mode, or stage files first)";
           }
-          case "all":
-            addCmd = "git add -A";
-            break;
-          case "tracked":
-          default:
-            addCmd = "git add -u";
-            break;
         }
 
         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 based on mode
+          if (mode === "all") {
+            run(["add", "-A"]);
+          } else if (mode === "tracked") {
+            run(["add", "-u"]);
+          }
+          // staged mode: nothing extra to add
+          const result = run(["commit", "-m", commitMsg]);
+          if (result.includes("command 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/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.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

@@ -2,14 +2,19 @@ import { z } from "zod";
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { existsSync, readFileSync } from "fs";
 import { join } from "path";
+import { execFileSync } from "child_process";
 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"] });
+    return true;
+  } catch {
+    return false;
+  }
 }
 
 export function registerSessionHandoff(server: McpServer): void {
@@ -44,7 +49,16 @@ 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"], {
+              encoding: "utf-8",
+              timeout: 10000,
+              stdio: ["pipe", "pipe", "pipe"],
+            }).trim();
+          } catch {
+            // gh not authenticated or no remote — skip
+          }
           if (openPRs && openPRs !== "[]") {
             sections.push(`## Open PRs\n\`\`\`json\n${openPRs}\n\`\`\``);
           }

src/tools/sharpen-followup.ts

@@ -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);