Claude Code ignores repository instructions after compaction

Structured summary

Symptoms

For the first hour or two of a session the agent follows CLAUDE.md faithfully. After the auto-compact fires (you'll see the context indicator reset), behaviour degrades: it starts using npm in a pnpm repo, runs `git commit` when CLAUDE.md says to always ask first, and re-reads files it was told to treat as generated. Asking 'what does CLAUDE.md say about commits?' gets a correct answer — it re-reads the file — and then it violates the same rule two tool calls later.

Likely cause

Compaction summarizes the conversation, and the summary preserves task state better than standing constraints. The CLAUDE.md content technically gets re-injected, but the dozens of turns where rules were actively applied are gone, so rule-following behaviour that was reinforced by conversation history resets to baseline. Worse after multiple compactions in one session.

Affected versions

2.2.0 – 2.4.1

Environments

Any long session; worst in large repos where sessions routinely hit the auto-compact threshold

Operating systems

macOS, Linux, Windows

Confidence

High confidence

Reproduction matrix