If you are working with PDE, JGit (or other dependencies) is best consumed through a Target Platform.
The definition below integrates JGit 3.2 from the projects' software repository at Eclipse.org.
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?pde version="3.8"?><target name="JGit" sequenceNumber="53">
<locations>
<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
<unit id="org.eclipse.jgit.feature.group" version="3.2.0.201312181205-r"/>
<unit id="org.eclipse.jgit.source.feature.group" version="3.2.0.201312181205-r"/>
<repository location="http://download.eclipse.org/egit/updates"/>
</location>
</locations>
</target>
Paste the snippet into a file within your workspace and open it with the (default) Target Definition Editor. Select the 'Set as Target Platform' link in the top-right corner. This will download JGit along with required bundles and make them your current target platform.