diff --git a/docs/execution/run-configuration.mdx b/docs/execution/run-configuration.mdx
index 27c330da9..82c947373 100644
--- a/docs/execution/run-configuration.mdx
+++ b/docs/execution/run-configuration.mdx
@@ -141,6 +141,10 @@ timeout_ms = 60000
 
 Each command must exit with status 0. If any command fails or times out, the run aborts before the workflow starts.
 
+<Note>
+When cloning repositories, always clone into a named subdirectory rather than the current directory (`.`). The current working directory may already contain files, causing `git clone` to fail with "destination path already exists and is not an empty directory". Use `git clone <url> <dirname>` instead.
+</Note>
+
 ### `[sandbox]`
 
 Configure how agent tools (bash, file edits) are executed.
@@ -488,4 +492,4 @@ Use `--preflight` to validate a run config without executing it:
 
 ```bash
 fabro run run.toml --preflight
-```
+```
\ No newline at end of file