comment on

the idea that you have power to change the structure of code and you should do it, keeps bothering you. What you should do?

Tread very carefully:

Does the code in question have a good set of regression tests? After all, your "improvements" may introduce new bugs in working code. How will that news be received? Without the safety net of a comprehensive test suite, refactoring legacy code is suicide.
How do you know your restructurings are "better" than the original code? Are you smarter than the original developers? Are you a better programmer? Do you understand the problem domain better? Do you have more time?

See also:

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laziness, impatience, and hubris
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