Thanks for the suggestions and the quick replies. I was able to edit our ant build scripts to get only the modified files and pass them into gjslint like so:
<!-- Get js files modified since last time we ran gjslint -->
<fileset dir="${js-src}" id="unlinted.files.ref">
<include name="**" /><!-- All Sub-directories -->
<include name="*.js" />
<date datetime="${gjslintTimestamp}" pattern="${tstamp.pattern}" when="after"/>
</fileset>
<pathconvert property="unlinted.files" refid="unlinted.files.ref" pathsep=" " />
Upon successful lint, the gjslintTimestamp build property gets updated.