By speeding up the process of narrowing down the possible reasons for bug or limitation, I try to enhance my workflow, resources and improve the quality of my work. I'm an Eclipse user and you could also check out NetBeans, Sublime, PhpStorm, Komodo or anything else with more capabilities. Using IDE helps you to set up connection between the codebase and version control, debugger, FTP and use number of function suggestions and PHPDoc comments while developing and browsing the code. By one and see if one of the plugins acts on the site when on off, Normally it narrows down to 2 steps, iterated and expressed depending on the scenario disable plugins one switch the theme.. See if you could find any errors in the logging plugins or the error log file they come up with stacktrace telling you the origin of the error including filename and number. you would be able to find area piece of code that exists in the problematic pages and not in all the others. It's common thing for frameworks such keeping the same naming convention and directory structure for placing files. Avoid using get posts or query posts in environment, better use custom WP Query query and reset the postdata at the end not to interfere with other listings.. However CSS selectors have priority, such as IDs are with priority than just classes, so keep that in mind .. You need to learn how to select the phrase for searching limit the results by the advanced filters, like limit by location, by date, use some wildcard like site intitle inurl filetype or anything that could help you limit the billions of results.
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