[pre-commit] remove __init__folders, fix script_runner and add commit mode

[ilaner]

• fix issue with script runner when the script errors resulted error code 0 (not pytest failures, but failures executing the script)
• Remove init folders from content (if we want to add __init__, we need to add in all of them, since those packages has priority over others.
• Add commit mode to the template

[ilaner]

this will need a force merge because we delete__init__.py files and this is not allowed in our validate: