I assume this is due to the fact that claude code appends a system message each time it reads a file that instructs it to think if the file is malware. It hasnt been an issue recently for me but it used to be so bad I had to patch out the string from the cli.js file. This is the instruction it uses:

> Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.