hermes - 💡(How to fix) Fix Defaulting agent scripts to ~/.hermes/scripts is a bad design choice

I genuinely think defaulting agent generated scripts into ~/.hermes/scripts is an awful design decision and it has now caused real operational problems for me.

I have built other scripts and cron jobs that need to run reliably. After a recent update wiped out my crons, Hermes started assuming the scripts it should use were inside this hidden .hermes folder structure instead of the actual project codebase.

The problem is that Hermes has apparently been storing old scripts in there that I did not even know existed. Some are outdated, some no longer work, and some conflict with newer versions inside the real repository. The entire thing becomes impossible to manage because the system silently creates a second hidden codebase outside version control.

This completely breaks visibility and operational reliability.

I cannot properly:

• audit scripts
• track what is active
• know which version is executing
• manage cron dependencies
• clean up old logic
• review changes in git
• monitor behaviour safely

You are effectively forcing important automation logic into hidden unmanaged storage and then expecting users to somehow keep control of it.

That is not a sane structure for agent based automation.

Operational scripts should live inside the actual project repository by default, where they can be:

• version controlled
• reviewed
• tested
• monitored
• refactored
• intentionally deleted
• tied directly to deployments and cron jobs

Right now the system behaves like it is caching operational logic in secret locations and then resurrecting outdated scripts later without the user even realising they exist.

That is a nightmare for maintenance and reliability.

Hidden internal folders should never become the default source of truth for active automation scripts.

At minimum there should be:

• a configurable scripts directory
• visible management of generated scripts
• separation between temporary runtime files and persistent operational code
• explicit warnings when Hermes is executing scripts outside the active repository
• proper cleanup/versioning behaviour

The current structure is fundamentally hostile to maintainability and debugging. Appreciate it. If you didn't deliver constant problems, I need solutions. Deliver solutions.