Fix/remove comment code

[Yubo-Cao]

Closes N/A

Steps to test

1. Removed some comment version controlled code
2. Handled error thrown after running set main file directory walkthrough (due to listeners not fully cleaned up)
3. Handled error thrown during walkthrough due to JavaFX node is null
4. Fixed transparent Popover arrow after getting compatible dark mode (please pardon me on hardcoding Base.css and Dark.css; it seems applying CSS variable of complex color is still somewhat of an issue).

Mandatory checks

• I own the copyright of the code submitted and I license it under the MIT license
• I manually tested my changes in running JabRef (always required)
• [/] I added JUnit tests for changes (if applicable)
• I added screenshots in the PR description (if change is visible to the user)
• [/] I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
• [/] I checked the user documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

[jabref-machine]

Note that your PR will not be reviewed/accepted until you have gone through the mandatory checks in the description and marked each of them them exactly in the format of [x] (done), [ ] (not done yet) or [/] (not applicable).

[trag-bot]

@trag-bot didn't find any issues in the code! ✅✨