Atlassian And New SSL Certificates

Or How CAs Drain Your Lifetime

When you check my activity, you simply can see, that the past weeks my time for writing was quite limited. Since I had a few very urgent projects, I had no time to care about my blog. But when it can get no worse, your website provider, that previously relied on the Symantec CA, decides to switch it’s root CA to some better and quite new CA that 1. is not listed in some JRA distributions‘ keystore and 2. uses trust chains with intermediate certificates. And this leads to an ugly situation when you run e.g. some Atlassian tool environment where the tools in turn use SSL to connect to each other. I would have not realized the problem so early, nor it would not have been so urgent, when I would not have decided to do all authentication (Bitbucket and Confluence) through JIRA’s Crowd-API.

But let’s start from the beginning… My provider, where I get my SSL certificate from (namely the german 1&1) used the Symantec CA for years. This CA somehow attracted Google’s anger, so Google decided to remove Symantec from the trusted CAs list of it’s chrome browser and announced this around beginning of 2018. 1&1 did not find a reason to get in hurry, so they kept their CA until mid of 2018. Then they started to remind their customers to update their SSL certificates, forcing their customers to hurry a lot. I realized, that there is some neccessity to follow their appeal, but I also felt to still have some time and do it, when the certificate expires…

Then the time came and my Chrome browser refused to show my Atlassian pages. So I logged in to my 1&1 Account and my Linux machine where JIRA & Co. runs, ordered a new SSL certificate, copy-pasted it into my Nginx configururation (which I use as an SSL proxy) and everything went fine at the first glance. I could log in to JIRA without a hassle, did not see any JIRA warnings or hovers and my browser also was not shouting at me about the SSL connection. Everything was fine. But then came the surprise… I tried to log into Confluence (no I currently have no SSO 🙁 ). I let the browser enter my credentials and… got refused. I tried some more times manually with different combinations of users and passwords, checked my password store, checked CAPS LOCK,… but I did not get in. Since I disabled the „local admin“ of Confluence (due to being tight on the 10 user limit), I could also not check from inside Confluence.

What happened? After digging (this is what I often do 😉 ) through the settings, I stumbled over the Application Links section, which stated, that the connection could not be established due to SSL errors. Ah, OK, nice that Atlassian is recommending to install the JIRA SSL Add-on that helps with all that suff. Really all? For sure, not! Especially not with problems I encounter 🙁 . After digging deeper and deeper, I found, that the new chain of trust, 1&1 uses, is not setup in the JIRA keystore, the atlassian tools ship with their JRE. In contrast Chrome’s certificate store is updated tightly.

How to fix? First you need to find the Java keystore to add the CA certificate to be trusted. This is quite a bit difficult, if you do not know about the tool’s shipped JRE. So don’t hassle around with your distributions keystore, step into the folder where your tools are install (/opt/atlassian/ in my case) and do a

find . -type f -name cacerts

In my case, the list shows as follows:


I know, Bitbucket 5.2.2 is quite old (and the other tools, too), but keeping it up-to-date is quite hard for a spare-time setup. I believe, with an up-to-date installation, the problem would not have encountered. Let’s see, when I update… With this knowledge, it is quite easy (and some manual work) to add your cert to the keystore.

To get the certificate from your server, just do a

bash$ openssl s_client -showcerts -servername -connect </dev/null | sed -ne '/-BEGIN CERTIFICATE-/,/-END CERTIFICATE-/p' > ${HOME}/

Then you can import that certificate into your Java keystore with the following command set (e.g. for confluence):

bash$ cd /opt/atlassian/jira/jre
bash$ bin/keytool -delete -alias \
-keystore lib/securety/cacerts -storepass changeit
bash$ bin/keytool -import -alias \
-keystore lib/securety/cacerts -storepass changeit \
-noprompt -file ${HOME}/

After doing that (I didn’t even need a restart of the tools), the application connections resurrect and you can log in to your confluence again.

The more convenient way is to write a little bash script that does the job. You can find mine here on Github. Feel free to improve it and issue some pull request if you think it’s worth to be shared.

Lessons learned

  1. Alsways keep a local admin account active in each and every Atlassian tool 😉
  2. Better use an automated SSL framework like Let’s encrypt. With it, you need to make the key rolling-update working from the beginning, not when it is too late (OK, this would not have helped me in my situation, nevertheless it is a good idea to do so)
  3. Document your problem solutions (which I do with scripts and this blog 🙂 )
  4. Don’t document the tool in the tool (e.g. this howto in Confluence), you will shoot both your feet 🙂
  5. Keep your tools up to date!

Windows (was) just a pain

Since I use Linux at home and love to develop embedded, backend and (web)-fronteds within a real operating system, I sometimes get crazy at work, when I just search for an alternative to a simple command line… So, what’s the alternative in Windows? The Command Prompt, then PowerShell or some specialized, magic, woodoo,… GUI application with the worst design ever seen in the universe and beyond?

OK, I see, you need an example 😉 Here it is one of my favorite: Syncronize a 100-GB-folder from one machine to another when one is at the end of the world, connected by avian carriers (see also RFC 2549 – IP over avian carriers) with a perceived rate of 2 bit per hour. 22 years ago, rsync was invented and serves every (unidirectional or pseude-bidirectional) syncronization desire with a sheer infinite amount of options… But, it is not available (directly) for windows…

Welp, some time ago, there was cygwin, which was driven by Red Hat. OK, it is still being developed, but somehow, I feel it is not serving my desires very well. At least not the desires a developer has. I also found MinGW and MSYS some years ago, but as I ran into trouble with wget and rsync when handling large files, I tested MSYS2 (it already includes MinGW-32 or MinGW-64, whichever you prefer). That was the starting point to test MSYS2 and to my surprise, it is exactly what makes my heart pound faster. All previous POSIX/Linux/Universe/Multiverse/… compatibility layers for Windows had some GUI to select packages, run updates,… But not MSYS2! It uses a pacman port. OK, I didn’t use pacman before when I was not forced to (I prefer APT), but it is COMMAND LINE and it runs on Windows (64-bit).

And even better, it did the ssh configuration well (a problem in old MSYS), so that you could generate and use an SSH key, which makes rsync even more powerful…

Hey guys of MSYS2, whenever you pass by in Germany (Erlangen), I will spend you some beer at Steinbach Bräu. This brewery is just to beer, what you are to Windows. Simply the greatest enrichtment 😉


So, if you would like to use rsync and wget in windows, just install MSYS2, do the obligatory update described on their page and execute the following:

pacman -S wget openssh rsync

Have fun with Bash, SSH, Rsync and all that other cool Linux tools on Windows!

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