From b926441e880774ea6998badeb97d7e5153b52c50 Mon Sep 17 00:00:00 2001
From: Jack Felke <jrinnfelke@gmail.com>
Date: Sat, 7 Mar 2026 19:45:42 -0700
Subject: [PATCH] fix: broken shell syntax in git.run() calls (checkpoint,
 what-changed, session-health)
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run() uses execFileSync which doesn't interpret shell operators (|, ||, &&,
2>/dev/null). These tools were passing shell pipelines/redirects as git args,
causing silent failures or incorrect results.

Fixed:
- what-changed: use getDiffFiles() helper and array args for log
- checkpoint: use array args for add/commit/reset instead of shell chains
- session-health: use array args for diff --stat, split output in JS

Same bug class as PR #170 (clarify-intent). Many more tools still affected —
see forthcoming issue for tracking.
---
 src/tools/checkpoint.ts     | 11 ++++++++---
 src/tools/session-health.ts |  3 ++-
 src/tools/what-changed.ts   |  7 ++++---
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/tools/checkpoint.ts b/src/tools/checkpoint.ts
index e086f01..d403395 100644
--- a/src/tools/checkpoint.ts
+++ b/src/tools/checkpoint.ts
@@ -84,11 +84,16 @@ ${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]);
+          if (addCmd !== "true") {
+            // Run the staging command (e.g. "add -u" or "add -A")
+            const addArgs = addCmd.replace(/^git\s+/, "").split(/\s+/);
+            run(addArgs);
+          }
+          const result = run(["commit", "-m", commitMsg]);
           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;
diff --git a/src/tools/session-health.ts b/src/tools/session-health.ts
index bd6a819..c3d859a 100644
--- a/src/tools/session-health.ts
+++ b/src/tools/session-health.ts
@@ -27,7 +27,8 @@ export function registerSessionHealth(server: McpServer): void {
       const dirtyCount = dirty ? dirty.split("\n").filter(Boolean).length : 0;
       const lastCommit = getLastCommit();
       const lastCommitTimeStr = getLastCommitTime();
-      const uncommittedDiff = run("git diff --stat | tail -1");
+      const fullDiffStat = run(["diff", "--stat"]);
+      const uncommittedDiff = fullDiffStat.split("\n").filter(Boolean).pop() || "";
 
       // Parse commit time safely
       const commitDate = parseGitDate(lastCommitTimeStr);
diff --git a/src/tools/what-changed.ts b/src/tools/what-changed.ts
index 913dfa2..2670422 100644
--- a/src/tools/what-changed.ts
+++ b/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, getDiffStat, getDiffFiles } 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);