Error while updating eclipse: Searching Alternate solutions - eclipse

Eclipse is throwing the following error when I check for updates:
An internal error occurred during: "Searching alternate solutions...".
org.codehaus.groovy.eclipse 2.6.1.xx-20120301-1300-e36-RELEASE is unknown in the solver!
I have searched and checked this related question, but I do not have the mentioned package installed. Neither anything is getting listed when I search for groo/java 8 etc in the installed software.
If I just ignore the groovy plugin update listed (and marked in error), and try to continue with the update, I am getting below error while updating software:
An error occurred while collecting items to be installed
session context was:(profile=epp.package.jee, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).
No repository found containing: osgi.bundle,org.codehaus.jackson.core,1.9.13
No repository found containing: osgi.bundle,org.codehaus.jackson.mapper,1.9.13
No repository found containing: osgi.bundle,org.eclipse.net4j.jms.api,3.0.0.v20110215-1551
No repository found containing: osgi.bundle,org.springframework.roo.wrapping.protobuf-java-lite,2.3.0.0001
Eclipse Version: Neon Release (4.6.0) and Build id: 20160613-1800
How do I fix this?
Installation Details from Eclipse:
Ansi Console 1.3.1.201508091828 net.mihai-nita.ansicon.feature.group Mihai Nita
Axis2 Tools 1.1.301.v201410160332 org.eclipse.jst.ws.axis2tools.feature.feature.group Eclipse Web Tools Platform
Cloud Foundry Tools Core 1.0.4.v201606021906 org.eclipse.cft.server.core.feature.feature.group Eclipse Tools for Cloud Foundry
Cloud Foundry Tools UI 1.0.3.v201606021906 org.eclipse.cft.server.ui.feature.feature.group Eclipse Tools for Cloud Foundry
Code Recommenders for Java Developers 2.4.0.v20160607-1609 org.eclipse.recommenders.rcp.feature.feature.group Eclipse Code Recommenders
Code Recommenders Mylyn Integration 2.4.0.v20160607-1609 org.eclipse.recommenders.mylyn.rcp.feature.feature.group Eclipse Code Recommenders
CXF Web Services 1.1.203.v201503151903 org.eclipse.jst.ws.cxf.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - Common 1.5.0.v201603181811 org.eclipse.jpt.common.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - EclipseLink Common 1.3.200.v201603180253 org.eclipse.jpt.common.eclipselink.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - EclipseLink DBWS Support 1.2.200.v201603180253 org.eclipse.jpt.dbws.eclipselink.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - EclipseLink JAXB Support 1.4.200.v201603180253 org.eclipse.jpt.jaxb.eclipselink.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - EclipseLink JPA Support 3.4.100.v201603180253 org.eclipse.jpt.jpa.eclipselink.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - JAXB Support 1.5.100.v201603180253 org.eclipse.jpt.jaxb.feature.feature.group Eclipse Web Tools Platform
Dali Java Persistence Tools - JPA Support 3.5.0.v201603181811 org.eclipse.jpt.jpa.feature.feature.group Eclipse Web Tools Platform
Data Tools Platform Connectivity 1.13.0.201603142002 org.eclipse.datatools.connectivity.feature.feature.group Eclipse Data Tools Platform
Data Tools Platform Connectivity Documentation 1.13.0.201603142002 org.eclipse.datatools.connectivity.doc.user.feature.group Eclipse Data Tools Platform
Data Tools Platform Enablement 1.13.0.201603142002 org.eclipse.datatools.enablement.feature.feature.group Eclipse Data Tools Platform
Data Tools Platform Intro 1.13.0.201603142002 org.eclipse.datatools.intro.feature.group Eclipse Data Tools Platform
Data Tools Platform Model Base 1.13.0.201603142002 org.eclipse.datatools.modelbase.feature.feature.group Eclipse Data Tools Platform
Data Tools Platform SQL Dev Tools Documentation 1.13.0.201603142002 org.eclipse.datatools.sqltools.doc.user.feature.group Eclipse Data Tools Platform
Data Tools Platform SQL Development Tools 1.13.0.201603142002 org.eclipse.datatools.sqldevtools.feature.feature.group Eclipse Data Tools Platform
Data Tools Platform Tutorial Documentation 1.13.0.201603142002 org.eclipse.datatools.common.doc.user.feature.group Eclipse Data Tools Platform
Data Tools Platform User Documentation 1.13.0.201603142002 org.eclipse.datatools.doc.user.feature.group Eclipse Data Tools Platform
Docker Tooling 2.0.0.201606101757 org.eclipse.linuxtools.docker.feature.feature.group Eclipse Linux Tools
EclEmma Java Code Coverage 2.3.3.201602231923 com.mountainminds.eclemma.feature.feature.group Mountainminds GmbH & Co. KG
Eclipse Faceted Project Framework 3.7.0.v201505072140 org.eclipse.wst.common.fproj.feature.group Eclipse Web Tools Platform
Eclipse Faceted Project Framework JDT Enablement 3.8.0.v201603091933 org.eclipse.jst.common.fproj.enablement.jdt.feature.group Eclipse Web Tools Platform
Eclipse Git Team Provider 4.4.0.201606070830-r org.eclipse.egit.feature.group Eclipse EGit
Eclipse Git Team Provider - Task focused interface 4.4.0.201606070830-r org.eclipse.egit.mylyn.feature.group Eclipse EGit
Eclipse IDE for Java EE Developers 4.6.0.20160613-1800 epp.package.jee Eclipse Packaging Project
Eclipse Java Development Tools 3.12.0.v20160606-1100 org.eclipse.jdt.feature.group Eclipse.org
Eclipse Java EE Developer Tools 3.8.0.v201605251556 org.eclipse.jst.enterprise_ui.feature.feature.group Eclipse Web Tools Platform
Eclipse Java Web Developer Tools 3.8.0.v201605120129 org.eclipse.jst.web_ui.feature.feature.group Eclipse Web Tools Platform
Eclipse Plug-in Development Environment 3.12.0.v20160606-1100 org.eclipse.pde.feature.group Eclipse.org
Eclipse Quicksearch 3.8.0.201606300730-RELEASE org.springsource.ide.eclipse.commons.quicksearch.feature.feature.group Pivotal Software, Inc.
Eclipse VJET JavaScript IDE (Incubation) 0.10.0.201303191704 org.eclipse.vjet.js.ide.feature.group Eclipse.org
Eclipse Web Developer Tools 3.8.0.v201606030549 org.eclipse.wst.web_ui.feature.feature.group Eclipse Web Tools Platform
Eclipse XML Editors and Tools 3.8.0.v201605120129 org.eclipse.wst.xml_ui.feature.feature.group Eclipse Web Tools Platform
Eclipse XSL Developer Tools 1.3.401.v201509231858 org.eclipse.wst.xsl.feature.feature.group Eclipse Web Tools Platform
EditBox 0.70.0.201508180438 pm.eclipse.editbox.feature.feature.group Nodeclipse
JavaScript Development Tools 2.0.0.v201605311817 org.eclipse.wst.jsdt.feature.feature.group Eclipse Web Tools Platform
JavaScript Development Tools Chromium/V8 Remote Debugger 0.4.0.v201606032110 org.eclipse.wst.jsdt.chromium.debug.feature.feature.group Eclipse Web Tools Platform
JAX-WS DOM Tools 1.0.302.v201504272154 org.eclipse.jst.ws.jaxws.dom.feature.feature.group Eclipse Web Tools Platform
JAX-WS Tools 1.2.203.v201602092125 org.eclipse.jst.ws.jaxws.feature.feature.group Eclipse Web Tools Platform
Jeeeyul's Themes 2.3.0.I20151022-090442 net.jeeeyul.eclipse.themes.feature.feature.group Jeeeyul#gmail.com
JSF Tools 3.9.0.v201605262035 org.eclipse.jsf.feature.feature.group Eclipse Web Tools Platform
JSF Tools - Tag Library Metadata (Apache Trinidad) 2.6.0.v201410101748 org.eclipse.jst.jsf.apache.trinidad.tagsupport.feature.feature.group Eclipse Web Tools Platform
JSF Tools - Web Page Editor 2.8.0.v201605262035 org.eclipse.jst.webpageeditor.feature.feature.group Eclipse Web Tools Platform
JSHint Eclipse Integration 0.10.1.20160216-0911 com.eclipsesource.jshint.feature.feature.group EclipseSource
JST Server Adapters 3.2.400.v201606081655 org.eclipse.jst.server_adapters.feature.feature.group Eclipse Web Tools Platform
JST Server Adapters Extensions 3.3.500.v201603031514 org.eclipse.jst.server_adapters.ext.feature.feature.group Eclipse Web Tools Platform
JST Server UI 3.4.300.v201606081655 org.eclipse.jst.server_ui.feature.feature.group Eclipse Web Tools Platform
LiClipseText Feature 1.0.0.201605191643 org.brainwy.liclipsetext.feature.feature.group Brainwy Software Ltda
m2e - Maven Integration for Eclipse (includes Incubating components) 1.7.0.20160603-1933 org.eclipse.m2e.feature.feature.group Eclipse.org - m2e
m2e - slf4j over logback logging (Optional) 1.7.0.20160603-1933 org.eclipse.m2e.logback.feature.feature.group Eclipse.org - m2e
m2e-wtp - JAX-RS configurator for WTP (Optional) 1.3.0.20160530-2310 org.eclipse.m2e.wtp.jaxrs.feature.feature.group Eclipse.org - m2e-wtp
m2e-wtp - JPA configurator for WTP (Optional) 1.3.0.20160530-2310 org.eclipse.m2e.wtp.jpa.feature.feature.group Eclipse.org - m2e-wtp
m2e-wtp - JSF configurator for WTP (Optional) 1.3.0.20160530-2310 org.eclipse.m2e.wtp.jsf.feature.feature.group Eclipse.org - m2e-wtp
m2e-wtp - Maven Integration for WTP 1.3.0.20160530-2310 org.eclipse.m2e.wtp.feature.feature.group Eclipse.org - m2e-wtp
Markdown Editor 1.2.0.201501260515 markdown.editor.feature.feature.group Winterwell
Minimalist Jade Editor 1.0.2.201509250223 org.nodeclipse.enide.editors.jade.feature.feature.group Nodeclipse/Enide
MoreUnit For Java 3.1.1 org.moreunit.feature.group MoreUnit.org
MoreUnit For Java: Mock Support 3.1.1 org.moreunit.mock.feature.group MoreUnit.org
MoreUnit Light 3.1.1 org.moreunit.light.feature.group MoreUnit.org
Mylyn Context Connector: Eclipse IDE 3.20.0.v20160421-1902 org.eclipse.mylyn.ide_feature.feature.group Eclipse Mylyn
Mylyn Context Connector: Java Development 3.20.0.v20160421-1902 org.eclipse.mylyn.java_feature.feature.group Eclipse Mylyn
Mylyn Task List 3.20.0.v20160608-1838 org.eclipse.mylyn_feature.feature.group Eclipse Mylyn
Mylyn Task-Focused Interface 3.20.0.v20160608-1905 org.eclipse.mylyn.context_feature.feature.group Eclipse Mylyn
Mylyn Tasks Connector: Bugzilla 3.20.0.v20160425-1835 org.eclipse.mylyn.bugzilla_feature.feature.group Eclipse Mylyn
Mylyn WikiText 2.9.0.v20160601-1831 org.eclipse.mylyn.wikitext_feature.feature.group Eclipse Mylyn
Nodeclipse ChromeDevTools SDK 0.3.9.201509250223 org.chromium.sdk.feature.group The Chromium Authors, Nodeclipse
Nodeclipse Chromium JavaScript Remote Debugger 0.3.9.201509250223 org.chromium.debug.feature.group The Chromium Authors, Nodeclipse
Nodeclipse Core and Node.js 1.0.2.201509250223 org.nodeclipse.feature.group Nodeclipse/Enide
Nodeclipse Git Addon 1.0.0.20140303-0606 gitaddon.feature.feature.group Nodeclipse organization
Nodeclipse Plugins List 1.0.2.201509250223 org.nodeclipse.pluginslist.feature.feature.group Nodeclipse organization
Remote System Explorer End-User Runtime 3.7.1.201603211627 org.eclipse.rse.feature.group Eclipse TM Project
Remote System Explorer User Actions 3.7.0.201603211627 org.eclipse.rse.useractions.feature.group Eclipse TM Project
SonarLint for Eclipse 2.1.0.20160603-1122-RELEASE org.sonarlint.eclipse.feature.feature.group SonarSource
SonarLint for Eclipse Java Configuration Helper 2.1.0.20160603-1122-RELEASE org.sonarlint.eclipse.jdt.feature.feature.group SonarSource
Spring IDE AOP Extension (optional) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.aop.feature.feature.group Spring IDE Developers
Spring IDE Autowire Extension (optional) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.autowire.feature.feature.group Spring IDE Developers
Spring IDE Batch Extension (optional) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.batch.feature.feature.group Spring IDE Developers
Spring IDE Boot Microservices Dash 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.boot.dash.feature.feature.group Spring IDE Developers
Spring IDE Core (required) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.feature.feature.group Spring IDE Developers
Spring IDE Integration, Flex and Web Services Extension (optional) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.integration.feature.feature.group Spring IDE Developers
Spring IDE Maven Support 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.maven.feature.feature.group Spring IDE Developers
Spring IDE Security Extension (optional) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.security.feature.feature.group Spring IDE Developers
Spring IDE Spring Data Support 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.data.feature.feature.group Spring IDE Developers
Spring IDE Web Flow Extension (optional) 3.8.0.201606301005-RELEASE org.springframework.ide.eclipse.webflow.feature.feature.group Spring IDE Developers
StartExplorer Feature 1.7.0 de.bastiankrol.startexplorer.feature.feature.group Bastian Krol
SWTend 2.2.5.I20140918-144458 net.jeeeyul.swtend.feature.feature.group jeeeyul#gmail.com
TM Terminal 4.1.0.201606052351 org.eclipse.tm.terminal.feature.feature.group Eclipse.org - Target Management
WST Server Adapters 3.2.500.v201606081655 org.eclipse.wst.server_adapters.feature.feature.group Eclipse Web Tools Platform

Try to delete all the update sites from the preferences, restart STS, and add them back, step by step to see when the error starts to appear.

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