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Javascript enqueue - Avoid javascript conflicts

Hi There,

I have built a custom wordpress theme and it seems that a lot of plugins are not compatible with the theme and I believe it has to do with javascript conflicts. (jquery and possibly others)

I am curious as to what is the absolute best way to include javascript in a custom wordpress theme to ensure that is is compatible with as many plugins as possible. (both the jquery library as well as custom javascript files I;ve included in the theme)

Currently the javascript is being called in header.php and footer.php.

I have red that using the enqueue is the best way to call in javascript, but I don't know a whole lot about this.

If possible, I would like to have all of my javascript references in an external file to keep things organized and keep my page header/footer nice and tidy.

Thanks a lot for your expert help.