Re-arrange folder structure

[CLHatch]

Pull request

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Approach
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Summary by Sourcery

Add a dedicated helper for safely setting file ownership and permissions and integrate it with the existing script runner.

New Features:

• Introduce a set_permissions helper script to manage ownership and permissions for target paths with basic safety checks.

Enhancements:

• Integrate the new set_permissions script with the existing run_script mechanism for consistent invocation across the project.

[sourcery-ai]

Reviewer's Guide

Refactors script organization by introducing a dedicated .scripts directory with a new set_permissions helper script and a small cleanup in run_script.sh, adding permission-setting logic with safety checks and a test hook.

Sequence diagram for invoking the new set_permissions script via test_set_permissions

sequenceDiagram
    actor User
    participant Shell
    participant test_set_permissions
    participant run_script
    participant set_permissions

    User ->> Shell: execute DockSTARTer tests
    Shell ->> test_set_permissions: call function
    test_set_permissions ->> run_script: run_script set_permissions
    run_script ->> set_permissions: source and execute function
    set_permissions ->> set_permissions: validate CH_PATH safety
    set_permissions ->> set_permissions: optionally chown and chmod CH_PATH
    set_permissions ->> set_permissions: ensure SCRIPTNAME is executable
    set_permissions -->> run_script: return
    run_script -->> test_set_permissions: return
    test_set_permissions -->> Shell: return

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File-Level Changes

Change	Details	Files
Introduce a reusable set_permissions helper script with safety checks around which paths can be modified and how ownership/permissions are applied.	Create .scripts/set_permissions.sh with set_permissions function that validates target path against system directories and home directory Add logic to warn when changing permissions outside the detected home directory and to skip known system paths Apply chown and chmod recursively to the target path when non-root PUID/PGID are detected, and ensure the main script is executable with proper error handling Define a test_set_permissions function that delegates to run_script 'set_permissions'	.scripts/set_permissions.sh
Minor cleanup in run_script to prepare or align with new script layout.	Remove an unnecessary blank line before the script existence check to keep formatting consistent	includes/run_script.sh

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[sourcery-ai]

Hey - I've left some high level feedback:

• The new set_permissions helper is placed under .scripts, but run_script still looks only in scripts/, so test_set_permissions calling run_script 'set_permissions' will fail unless you either move the script into scripts/ or update run_script to also search .scripts.
• Having set_permissions unconditionally invoke sudo makes it harder to reuse in non-interactive or constrained environments; consider honoring an existing SUDO/DS_SUDO wrapper or adding a way to disable sudo for callers that already run with appropriate privileges.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The new `set_permissions` helper is placed under `.scripts`, but `run_script` still looks only in `scripts/`, so `test_set_permissions` calling `run_script 'set_permissions'` will fail unless you either move the script into `scripts/` or update `run_script` to also search `.scripts`.
- Having `set_permissions` unconditionally invoke `sudo` makes it harder to reuse in non-interactive or constrained environments; consider honoring an existing `SUDO`/`DS_SUDO` wrapper or adding a way to disable `sudo` for callers that already run with appropriate privileges.

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