You can add all your javascript files to the js folder in your theme like:
sample-theme/docroot/_diffs/js/jquery-1.8.2.min.js
And then to make it available for everybody you can write any of the following lines in the <head> section of the template files portal_normal.vm and portal_pop_up.vm present in the directory sample-theme/docroot/_diffs/templates/:
#js ("$javascript_folder/jquery-1.8.2.min.js")
Or
<script src="$javascript_folder/jquery-1.8.2.min.js"></script>
Note: portal_pop_up.vm is for applying your javascript changes to AUI dialog pop-ups, if you are using them
Some more explanation as to how things work:
$javascript_folder is a velocity variable present in the theme's template files which points to the javascript storage path (default is: ${root-path}/js) which can be defined in the liferay-look-and-feel.xml like this:
<theme id="sample" name="Sample">
<root-path>/html</root-path> <!-- optional -->
<javascript-path>${root-path}/js/jQuery</javascript-path> <!-- So path becomes: sample-theme/html/js/jQuery -->
</theme>
You can also customize ${root-path} just like <javascript-path> by specifying it in liferay-look-and-feel.xml as <root-path> as shown. The default value of ${root-path} is / i.e. it refers to the directory sample-theme/.
Basically the folders css, js, templates & images are the ones which gets updated with the changes you make in the corresponding _diffs folder (_diffs/css, _diffs/js etc) when you build the theme. So that is the reason the velocity variables like $javascript_folder & $css_folder point to sample-theme/js & sample-theme/css respectively instead of sample-theme/_diffs/js or sample-theme/_diffs/css.
Hope this helps.