JIRA won't start after installing and configuring SSL certificate

[Alejandro Suárez García]

Hi all.

We have been following this guide:

https://confluence.atlassian.com/adminjiraserver071/running-jira-applications-over-ssl-or-https-802593051.html

We used Thawte SSL evaluation certificate. After installing and configuring the certificates, the Atlassian JIRA Service won't start. We also followed this guide:

https://confluence.atlassian.com/jirakb/jira-throws-severe-message-during-startup-due-to-unable-to-create-directory-for-deployment-389781040.html?_ga=2.66118510.1763018003.1505111144-1577165473.1503587437

Can you please help me? 

And this is a part of Catalina log, the total log has 84k characters and maximum is 20k

13-Sep-2017 14:41:24.436 ADVERTENCIA [main] org.apache.catalina.startup.SetAllPropertiesRule.begin [SetAllPropertiesRule]{Server/Service/Connector} Setting property 'sslProtocol' to 'TLS' did not find a matching property.
13-Sep-2017 14:41:24.436 ADVERTENCIA [main] org.apache.tomcat.util.IntrospectionUtils.setProperty IntrospectionUtils: InvocationTargetException for class org.apache.catalina.connector.Connector useBodyEncodingForURI=true)
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:126)
at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:47)
at org.apache.catalina.startup.SetAllPropertiesRule.begin(SetAllPropertiesRule.java:66)
at org.apache.tomcat.util.digester.Digester.startElement(Digester.java:1190)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:182)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1458)
at org.apache.catalina.startup.Catalina.load(Catalina.java:578)
at org.apache.catalina.startup.Catalina.load(Catalina.java:629)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: java.lang.NullPointerException
at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:60)
at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:47)
at org.apache.catalina.connector.Connector.setProperty(Connector.java:282)
at org.apache.catalina.connector.Connector.setUseBodyEncodingForURI(Connector.java:746)
... 28 more

13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:C:\Program Files\Atlassian\JIRA\logs\atlassian-jira-gc-%t.log
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=C:\Program Files\Atlassian\JIRA
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=C:\Program Files\Atlassian\JIRA
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=C:\Program Files\Atlassian\JIRA\temp
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=C:\Program Files\Atlassian\JIRA\conf\logging.properties
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: exit
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms256m
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx768m
13-Sep-2017 14:41:24.451 INFORMACIÓN [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent La biblioteca nativa de Apache Tomcat basada en ARP que permite un rendimiento óptimo en entornos de desarrollo no ha sido hallada en java.library.path: C:\Program Files\Atlassian\JIRA\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Program Files\PHP\v7.1;C:\Program Files (x86)\Google\Chrome\Application;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Users\Administrador.WIN-3MEGL54HBBO\AppData\Local\Microsoft\WindowsApps;%JAVA_HOME%\bin;C:\Windows\system32\config\systemprofile\AppData\Local\Microsoft\WindowsApps;.
13-Sep-2017 14:41:24.733 INFORMACIÓN [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
13-Sep-2017 14:41:24.920 INFORMACIÓN [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
13-Sep-2017 14:41:24.920 GRAVE [main] org.apache.catalina.core.StandardService.initInternal No pude inicializar el conector [Connector[org.apache.coyote.http11.Http11Protocol-8443]]
org.apache.catalina.LifecycleException: Failed to initialize component [Connector[org.apache.coyote.http11.Http11Protocol-8443]]
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:873)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
at org.apache.catalina.startup.Catalina.load(Catalina.java:606)
at org.apache.catalina.startup.Catalina.load(Catalina.java:629)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: java.lang.NullPointerException
at org.apache.tomcat.util.IntrospectionUtils.getProperty(IntrospectionUtils.java:189)
at org.apache.catalina.connector.Connector.getProperty(Connector.java:266)
at org.apache.catalina.connector.Connector.createObjectNameKeyProperties(Connector.java:860)
at org.apache.catalina.connector.Connector.getObjectNameKeyProperties(Connector.java:1057)
at org.apache.catalina.util.LifecycleMBeanBase.initInternal(LifecycleMBeanBase.java:61)
at org.apache.catalina.connector.Connector.initInternal(Connector.java:915)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
... 12 more

13-Sep-2017 14:41:25.717 GRAVE [Catalina-startStop-1] org.apache.catalina.core.ContainerBase.startInternal A child container failed during start
java.util.concurrent.ExecutionException: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:911)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:890)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1403)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1393)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
... 6 more
Caused by: java.lang.NullPointerException
at org.apache.tomcat.util.IntrospectionUtils.getProperty(IntrospectionUtils.java:189)
at org.apache.catalina.connector.Connector.getProperty(Connector.java:266)
at org.apache.catalina.connector.Connector.getAttribute(Connector.java:293)
at org.apache.catalina.core.ApplicationContext.populateSessionTrackingModes(ApplicationContext.java:946)
at org.apache.catalina.core.ApplicationContext.<init>(ApplicationContext.java:123)
at org.apache.catalina.core.StandardContext.getServletContext(StandardContext.java:2240)
at org.apache.catalina.core.StandardContext.postWorkDirectory(StandardContext.java:6110)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 6 more

13-Sep-2017 14:41:25.717 GRAVE [main] org.apache.catalina.core.ContainerBase.startInternal A child container failed during start
java.util.concurrent.ExecutionException: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost]]
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:911)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:422)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:791)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.startup.Catalina.start(Catalina.java:655)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1403)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1393)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.catalina.LifecycleException: A child container failed during start
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:890)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 6 more

13-Sep-2017 14:41:25.717 GRAVE [main] org.apache.catalina.startup.Catalina.start The required Server component failed to start so Tomcat is unable to start.
org.apache.catalina.LifecycleException: Failed to start component [StandardServer[8005]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
at org.apache.catalina.startup.Catalina.start(Catalina.java:655)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardService[Catalina]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:791)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 7 more
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:422)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 9 more
Caused by: org.apache.catalina.LifecycleException: A child container failed during start
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 11 more

13-Sep-2017 14:41:25.717 GRAVE [main] org.apache.catalina.connector.Connector.pause Ha fallado la pausa del manejador de protocolo
java.lang.NullPointerException
at org.apache.catalina.connector.Connector.pause(Connector.java:891)
at org.apache.catalina.core.StandardService.stopInternal(StandardService.java:467)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
at org.apache.catalina.core.StandardServer.stopInternal(StandardServer.java:812)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
at org.apache.catalina.startup.Catalina.start(Catalina.java:659)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

13-Sep-2017 14:41:25.733 GRAVE [main] org.apache.catalina.core.StandardService.destroyInternal Failed to destroy connector [Connector[org.apache.coyote.http11.Http11Protocol-8443]]
org.apache.catalina.LifecycleException: Failed to destroy component [Connector[org.apache.coyote.http11.Http11Protocol-8443]]
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:302)
at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:571)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:881)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
at org.apache.catalina.startup.Catalina.start(Catalina.java:659)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
Caused by: org.apache.catalina.LifecycleException: Falló la destrucción del manejador de protocolo
at org.apache.catalina.connector.Connector.destroyInternal(Connector.java:1008)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
... 11 more
Caused by: java.lang.NullPointerException
at org.apache.catalina.connector.Connector.destroyInternal(Connector.java:1006)
... 12 more

[Andy Heinzer · Accepted solution]

There is a known bug in JIRA 7.3.x and higher that is causing this error message.   Please see https://jira.atlassian.com/browse/JRASERVER-63734 for details.

JIRA is using Tomcat to host its website.  However starting with JIRA 7.3.0 and above, we're using a newer version of Tomcat that no longer supports the old org.apache.coyote.http11.Http11Protocol

To make matters worse, the JIRA Config Utility is still setup to use that protocol even though it won't work with these newer JIRA versions.  Another bug for that one in https://jira.atlassian.com/browse/JRASERVER-64037

But you can manually edit the $JIRA_INSTALL/conf/server.xml file in order to change this protocol to fix this.  Right now your connector for SSL looks something like this:

<Connector port="8443" protocol="org.apache.coyote.http11.Http11Protocol"
              maxHttpHeaderSize="8192" SSLEnabled="true"
              maxThreads="150" minSpareThreads="25"
              enableLookups="false" disableUploadTimeout="true"
              acceptCount="100" scheme="https" secure="true"
              clientAuth="false" sslProtocol="TLS" useBodyEncodingForURI="true"
              keyAlias="jira" keystoreFile="<JIRA_HOME>/jira.jks" keystorePass="changeit" keystoreType="JKS"/>

What you need to do is change it to look like this:

<Connector port="8443" protocol="org.apache.coyote.http11.Http11NioProtocol"
              maxHttpHeaderSize="8192" SSLEnabled="true"
              maxThreads="150" minSpareThreads="25"
              enableLookups="false" disableUploadTimeout="true"
              acceptCount="100" scheme="https" secure="true"
              clientAuth="false" sslProtocol="TLS" useBodyEncodingForURI="true"
              keyAlias="jira" keystoreFile="<JIRA_HOME>/jira.jks" keystorePass="changeit" keystoreType="JKS"/>

By changing that protocol to use the org.apache.coyote.http11.Http11NioProtocol you can then save that file, and restart JIRA.  This should allow JIRA to at least start up when configured to server content over SSL/HTTPS.

This problem is very common to see and in turn is mentioned in the JIRA 7.3 upgrade notes.

[Alejandro Suárez García]

Thank you, It did work.

[JiraYo]

Are you kidding me? WTF... this bug was from sept and you havent fixed it yet? i spent like an hour trying to figure out why it wouldn't bind to port 443 and just happened upon this. You need to update your release so that this works out of the box. Any change i make with the config program resets this attribute as well so i guess im not using config.bat anymore..  pretty sloppy atlassian!

This is something that just about everyone is going to want to do to their instance. Especially as in my case, if you have plugins that require https to work properly...

[Dzintars]

Thank you so MUCH!!!

Finally after some week of fighting I solved issue! This is crazy how few simple steps is made so difficult.

This instruction and Yours instruction made SSL enabled. Icons also are delivered under https.

[Nic Brough -Adaptavist-]

You do know that "this instruction" simply parrots the Atlassian documentation?

It's wrong for Jira 7.3 because of the bug Andrew mentions, but that's the exception.

[Dzintars]

In my case "This instruction" helped the most, because contains full setup in normal human language. Step by step. None of 187 other Atlassians SSL setup instructions helped for me. And as i saw in forums, i am not the only person who is fighting with this setup long days. So there is definitely something wrong with instructions.

I just posted what was working for me.

After this setup SSL was working well, but Application Links cant be set up.

So i figured out that the problem was in cacert files and most easiest way is to install unsupported SSL Plugins for Jira and Confluence.

So finally, after some weeks i have fully functioning https://jira.domain.com and https://confluence.domain.com with all Application Links working.
If somebody need help - feel free to contact me.

[Nic Brough -Adaptavist-]

I'm not saying it doesn't work, I'm just pointing out that it tells you to do the same things the Atlassian docs tell you to do. 

I can't explain why you struggled with one set of docs and were ok with a copy and pasted version.

[JiraYo]

Writers of documentation often don't think like users.

For one, the stack exchange doc links actual real world configs, so you can see where yours is falling apart. I wrote a detailed step by step for this as well, as the jira docs dont cover importing and using your own certificate, for example.

If the official docs leave you with a broken instance, do you actually think its a problem with the users?