Trying to install on Eclipse 4.6 on OSX El Capitan:
An error occurred during the org.eclipse.equinox.internal.p2.engine.phases.CheckTrust phase.
session context was:(profile=epp.package.jee, phase=org.eclipse.equinox.internal.p2.engine.phases.CheckTrust, operand=, action=).
Error reading signed content.
Exception in opening zip file: /Applications/Developer/Eclipse.46.app/Contents/Eclipse/plugins/net.sf.eclipsecs.branding_6.19.1.201607051943.jar
Are you installing from the update site/market place? If so, please try installing from the packaged update site archive, as described here (section "From an update site archive"): http://eclipse-cs.sourceforge.net/#!/install
The error message "Exception in opening zip file" might hint at a corrupted download, but I don't have any Apple machine at hand to verify the installation procedure.
I tried, unfortunately with exactly the same result. I wonder if it might be Eclipse bug, OTOH other plugins did install well. Is there something I can do (debug?) to help you fix the problem?
I have the exact same problem on Windows 10 Pro (64-bit), using Eclipse Neon JEE (4.6.0), so this is not an Apple problem. The "net.sf.eclipsecs.branding_6.19.1.201607051943.jar" and "net.sf.eclipsecs.doc_6.19.1.201607051943.jar" files are actually HTML files with the title "SourceForge - Download Problem". Once the update site/market place install has failed it is not possible to install from the packaged update site. One must first revert to a previous installation configuration.
Last edit: Andrew Cottrell 2016-07-25
I just retried on a fresh Eclipse Neon installation and all worked as expected.
As Andrew pointed out the file content of the jars in question was in your case actually a HTML file. This seems to indicate that there was a Sourceforge infrastructure issue at the time of your install, which led to Sourceforge delivering a HTML page instead of the actual content (and not a HTTP error as one would expect...).
In any case the issue appears to have been temporary.
I suggest you go with Andrews recommendation by reverting the eclipse installation to a previous configuration (via Help->Installation details->Installation history).
Reverting and installing worked. Thanks!