Add usage note about bypass permissions mode

Author: schulzchristian

README.md

@@ -14,6 +14,10 @@ Algorithm Engineering, as defined by [Sanders (2009)](https://doi.org/10.1007/97
 
 Agentic Algorithm Engineering takes this methodology and hands the cycle to an autonomous AI agent. The agent formulates hypotheses, implements changes, runs experiments, and evaluates results, iterating continuously without human intervention. This allows systematic, high-throughput exploration of the optimization space while maintaining the scientific rigor of the AE methodology.
 
+## Usage
+
+The agent must run in a mode that does not require user input, since the AE cycle is designed to run autonomously and indefinitely. If you are using Claude Code, launch it with `--dangerously-skip-permissions` (byPassPermissions mode). For other agent frameworks, ensure that all tool calls (file edits, shell commands, git operations) are auto-approved so the loop can proceed without interruption.
+
 ## Author
 
 Christian Schulz, [Algorithm Engineering Group](https://ae.ifi.uni-heidelberg.de/), Heidelberg University