Fix bitrot issues due to updated Verilator and Python versions

[MikeOpenHWGroup]

Hi @Uzair-90, while reviewing your PR (#2631), I noticed a few other (non-fatal) issues. Please have a look at these and let me know what you think.

[Uzair-90]

This is a solid cleanup, the build system is now easier to maintain and more flexible. Using ?= lets people override settings without editing the Makefile, quoting in find makes it safer, and splitting the flags makes things clearer. The only thing to check is whether any CI scripts still use the old VERI_FLAGS name. But I think if all the tests are passed we are good.

[Uzair-90]

It very clean makes regex intent clear and avoids issues with backslash escaping.

[Uzair-90]

Switching the regex patterns to raw strings makes them clearer and avoids any issues with escape sequences. The Makefile updates are a solid improvement variables can now be overridden more easily, the compile and run flags are separated for clarity, and quoting in the find commands makes things safer.
The only thing worth double-checking is whether any scripts or CI jobs still reference the old VERI_FLAGS name, since that’s now VERI_RUN_FLAGS. Other than that, this is a clean, safe, and maintainable refactor. But I think if all tests are passed we are good for now.

[MikeOpenHWGroup]

Hi @Uzair-90, I deliberately merged in your PR (#2631) knowing that it would create a merge conflict. Once you've indicated that your PR resolves #2630, I will fix the conflicts here and request another review from you.

[Uzair-90]

Hi @MikeOpenHWGroup I have closed issue #2630 as the PR was merged. Please go on with the changes and you can assign me the review.

[MikeOpenHWGroup]

OK @Uzair-90, I have resolved the merge conflict. Please have a look (and thanks!).