Claude Code System Prompts Updated: New File Modification Reminder & REPL Clarifications, Malware Analysis Reminder Removed

Two new releases of the Claude Code (CC) system prompt are out: v2.1.124 and v2.1.126. Together they add 166 tokens and remove 87 tokens respectively. Here's what changed.

v2.1.124 — Additions (+166 tokens)

• File modification detection reminder: When the user or a linter changes a file but the diff is omitted because other modified files already exceeded the snippet budget, the agent now gets a system reminder: "File modification detected (budget exceeded)". The agent is directed to read the file if current content is needed.
• Harness instructions: The core-identity function call is replaced with explicit introductory-line and security-note insertion points before the shared harness instructions. This means you can now inject custom intro lines and security notes directly into the harness preamble.
• REPL tool usage clarification: The prompt now explicitly states that thenable shorthand results are auto-awaited only at return time. For inline uses—like concatenation, template literals, or passing as arguments to another call—you must explicitly await the thenable first.

v2.1.126 — Removals (-87 tokens)

• Malware analysis reminder removed: The system reminder that asked agents to consider whether each file read is malware and to analyze malware without improving or augmenting it has been removed. This frees up 87 tokens and suggests a shift in how the system handles security analysis.

Practical Impact

For developers using Claude Code (or building on its system prompt), these updates change how agents handle file diffs, harness configuration, and REPL scripting. If you rely on the core-identity function, you'll need to adapt to the new harness insertion points. The REPL clarification is critical: failing to await thenables in inline expressions can lead to subtle bugs.