I use similar workflow. Here is my refactoring and code quality prompt that I regularly run:

    Perform a thorough analysis of the <project_name> project (the code and the documentation).
    - Explore the project, go over all important files one by one and look for any mistakes or possible bugs.
    - Look for refactoring opportunities and ways to improve code quality and organization.
    - Identify any potential cruft/bloat, to ensure our code is clean and logically laid out. Keep in mind that efficient and good quality code needs to avoid over-engineered constructs and needless complexity. Avoid complicated logic where simple solutions would be more elegant.
    - Pay attention to comments: There should be enough of them to document the intent and provide high-level overview of the code logic, but not too much; avoid/remove excessive comments that simply restate the code logic or do not provide any useful information.
      - Every important function should have a top-level docstring comment that clearly explains its purpose, high-level logic overview, arguments, and return values.
    - Analyze the names of constants/variables/functions/classes and other code elements: could some of them be renamed to make their purpose more clear?
    - Analyze the documentation, uncover any potential inaccuracies/omissions and ensure the docs reflect the code.
    - Brainstorm ideas for improvements of the code and docs.
    
    After you finish the analysis, save an analysis report into "<project_name>_analysis_report.md" in the project root folder.