http://download.jboss.org/jbosstools/updates/nightly/core/trunk/plugins/ has no source plugins.
http://download.jboss.org/jbosstools/updates/nightly/core/trunk/features/ has no source plugins.

1. Add the missing source features to the aggregate sites:

core (site) :: http://download.jboss.org/jbosstools/updates/nightly/core/trunk/
soa-tooling (soa-site) :: http://download.jboss.org/jbosstools/updates/nightly/soa-tooling/trunk/
webtools :: http://download.jboss.org/jbosstools/updates/nightly/webtools/trunk/ /if applicable/

coretests :: http://download.jboss.org/jbosstools/updates/nightly/coretests/trunk/
soatests :: http://download.jboss.org/jbosstools/updates/nightly/soatests/trunk/

2. Remove this folder and associated Jenkins job(s):

~/trunk/build/aggregate/site/sources/

3. Add source features/plugins to JBDS sites too:

product :: http://www.qa.jboss.com/binaries/RHDS/builds/staging/devstudio-5.0_trunk.updatesite/product/ and http://www.qa.jboss.com/binaries/RHDS/builds/staging/devstudio-5.0_trunk.product/updates/nightly/trunk/
product-soa :: http://www.qa.jboss.com/binaries/RHDS/builds/staging/devstudio-5.0_trunk.soa-tooling.updatesite/product-soa/
extras :: http://www.qa.jboss.com/binaries/RHDS/builds/staging/devstudio-5.0_trunk.updatesite/extras/ /if applicable/