Yes, you can. But i think you should use inbox Magento tools in shell folder.
1. You need to disable compiler via admin or by shell command
cd /var/www/magento_root/ or else
php -f shell/compiler.php -- disable
- After that check the status of compiler
php -f shell/compiler.php -- state
You can see something like this
Compiler Status: Disabled
Compilation State: Compiled
Collected Files Count: 9165
Compiled Scopes Count: 4
As you can see your compiler process disabled now, but you have "Collected Files" in magento_root/include/src
For remove these files and folder use next:
php -f shell/compiler.php -- clear
Finally check status again:
php -f shell/compiler.php -- state
Now you see
Compiler Status: Disabled
Compilation State: Not Compiled
Collected Files Count: 0
Compiled Scopes Count: 0
Then look at the magento_root, folder include doesn't exist.