Update:

/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/security/cacerts is linked to /etc/ssl/certs/java/cacerts

Running

$keytool -list -v -keystore /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/security/cacerts > openjdkcacerts.txt

gives the linked...

http://pastebin.com/tc794cvP

So it seems java has access to all the necessary root CAs...

Update 2:

Tried jbdevstudio-product-universal-6.0.1.GA-v20130327-2052-B361.jar with the same result.

Install fails on the last step with:

"

One or more certificates rejected. Cannot proceed with installation.

Application failed, log file location: /home/user/oldjbdevstudio/studio/p2/director/configuration/1396768486738.log

"

The corresponding full log entry:

"

!SESSION 2014-04-06 12:44:46.503 -----------------------------------------------

eclipse.buildId=unknown

java.version=1.7.0_51

java.vendor=Oracle Corporation

BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_IN

Framework arguments:  -roaming -r jar:file:///home/sysadmin/Downloads/jbdevstudio-product-universal-6.0.1.GA-v20130327-2052-B361.jar!/ -d /home/sysadmin/oldjbdevstudio/studio -p jbds -i com.jboss.jbds.all,org.testng.eclipse.feature.group -profileProperties org.eclipse.update.install.features=true

Command-line arguments:  -roaming -r jar:file:///home/sysadmin/Downloads/jbdevstudio-product-universal-6.0.1.GA-v20130327-2052-B361.jar!/ -d /home/sysadmin/oldjbdevstudio/studio -p jbds -i com.jboss.jbds.all,org.testng.eclipse.feature.group -profileProperties org.eclipse.update.install.features=true

!ENTRY org.eclipse.equinox.p2.engine 8 0 2014-04-06 12:45:40.261

!MESSAGE One or more certificates rejected. Cannot proceed with installation.

"

Solved...

The org.eclipse.equinox.p2.engine JAR contained in the jbdevstudio-product-eap-universal-7.1.1.GA-v20140314-2145-B688.jar has a ECLIPSE_.RSA certificate that is signed by the root CA "GTE CyberTrust Solutions" but that root CA is not present in the openjdk cacerts (via openssl as described above):

"

$openssl pkcs7 -in ECLIPSE_.RSA -print_certs -inform DER

subject=/C=US/O=GTE Corporation/OU=GTE CyberTrust Solutions, Inc./CN=GTE CyberTrust Global Root

issuer=/C=US/O=GTE Corporation/OU=GTE CyberTrust Solutions, Inc./CN=GTE CyberTrust Global Root

-----BEGIN CERTIFICATE-----

"

But

$keytool -list -v -keystore /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/security/cacerts | grep GTE

produces no results

But I have the GTE root CA cert available in /usr/share/ca-certificates/mozilla/ so the steps to take are

a. Go to /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/security/

b. #mv cacerts oldcacertsold

c. #cp /etc/ssl/certs/java/cacerts .

d. #keytool -keystore /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/security/cacerts -importcert -alias GTECyberTrustGlobalRoot -file /usr/share/ca-certificates/mozilla/GTE_CyberTrust_Global_Root.crt

Now running java -jar jbdevstudio-product-eap-universal-7.1.1.GA-v20140314-2145-B688.jar works without errors...

Now I just need to figure out how to use the bloody thing... It's as complex as a space shuttle control panel!