Fixes https://github.com/modelcontextprotocol/modelcontextprotocol/security/code-scanning/21

CodeQL flagged execSync with interpolated file paths as CWE-78/CWE-88 shell command injection.

The issue

execSync(`npx prettier --write ${filesToFormat.join(" ")}`, { stdio: "inherit" });

The paths are derived from __dirname + SEP filenames, so direct exploitability requires commit access to seps/ — at which point you could just modify the script directly. But the bug is real:

• A path with spaces breaks the command (/home/user/my project/docs/seps/foo.mdx becomes two args)
• A SEP filename containing ; or $() would execute arbitrary commands (the filename regex ^(\\d+)-(.+)\\.md$ allows anything in .+)

The fix

execFileSync(npx, ["prettier", "--write", ...filesToFormat], { stdio: "inherit" });

Paths are passed as separate process arguments — never touch a shell. The process.platform === "win32" ? "npx.cmd" : "npx" resolution keeps it cross-platform.

Tested

$ npm run check:seps     # exit 0 (line 397 path)
$ npm run generate:seps  # exit 0, no diff in docs/ (line 437 path — formatting byte-identical)

Fixed both occurrences — line 395 had the identical pattern but the alert only flagged line 435.

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Checklist

• My changes follow the project's style guidelines
• I have performed a self-review of my changes
• Tested locally (check:seps + generate:seps)