Hi freeipa experts.

I have been using freeipa for the past 5 years running in a docker container, 
no replicas.
currently  on VERSION: 4.9.6, API_VERSION: 2.245

I have the following issue, not sure what caused this: pki-tomcat service is 
not starting, and it is no longer possible to login through the web-ui.
Auth through ldap (some websites) and through sssd on linux servers is still 
working, kerberos tickets are generated when logging with password or when 
running kinit, so critical operations are still possible.

The messages in `systemctl status pki-tomcatd@pki-tomcat.service` are
```
Apr 12 13:50:33 ipa.domain.com ipa-pki-wait-running[17869]: 
ipa-pki-wait-running: Request failed unexpectedly, 404 Client Error:  for url: 
http://ipa.domain.com:8080/ca/admin/ca/getStatus
Apr 12 13:50:34 ipa.domain.com systemd[1]: pki-tomcatd@pki-tomcat.service: 
start-post operation timed out. Terminating.
Apr 12 13:50:34 ipa.domain.com systemd[1]: pki-tomcatd@pki-tomcat.service: 
Control process exited, code=killed, status=15/TERM
Apr 12 13:50:34 ipa.domain.com systemd[1]: pki-tomcatd@pki-tomcat.service: 
Failed with result 'timeout'.
Apr 12 13:50:34 ipa.domain.com systemd[1]: Failed to start PKI Tomcat Server 
pki-tomcat.
```

journalctl give other errors (filtered what seems relevant).
```
Apr 12 13:49:05 ipa.domain.com server[17868]: WARNING: Problem with JAR file 
[/usr/share/pki/server/common/lib/commons-collections.jar], exists: [false], 
canRead: [false]
Apr 12 13:49:07 ipa.domain.com java[17868]: usr/lib/api/apiutil.c Could not 
open /run/lock/opencryptoki/LCK..APIlock
Apr 12 13:49:18 ipa.domain.com server[17868]: SEVERE: Context [/acme] startup 
failed due to previous errors

```


`/var/log/pki/pki-tomcat/pki/debug.2024-04-12.log`
contains the following errors 
```
2024-04-12 15:01:12 [main] SEVERE: Exception initializing random number 
generator using provider [Mozilla-JSS]
java.security.NoSuchProviderException: no such provider: Mozilla-JSS
        at 
java.base/sun.security.jca.GetInstance.getService(GetInstance.java:83)
        at 
java.base/sun.security.jca.GetInstance.getInstance(GetInstance.java:206)
....
```

`/var/log/pki/pki-tomcat/ca/debug.2024-04-12.log`
contains the following type of errors

```
2024-04-12 00:17:37 [main] SEVERE: Unable to start CA engine: Property 
instanceRoot missing value
Property instanceRoot missing value
        at 
com.netscape.cmscore.base.PropConfigStore.getString(PropConfigStore.java:297)
        at 
com.netscape.cmscore.apps.EngineConfig.getInstanceDir(EngineConfig.java:55)
        at com.netscape.cmscore.apps.CMSEngine.loadConfig(CMSEngine.java:233)
        at com.netscape.cmscore.apps.CMSEngine.start(CMSEngine.java:1025)
....

2024-04-12 17:49:21 [main] SEVERE: Exception sending context initialized event 
to listener instance of class [org.dogtagpki.server.ca.CAEngine]
java.lang.RuntimeException: Unable to start CA engine: Property instanceRoot 
missing value
        at 
com.netscape.cmscore.apps.CMSEngine.contextInitialized(CMSEngine.java:1672)
        at 
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4768)
        at 
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5230)
```

`getcert list` reports all entries except the caCACert as expired.

I tried pretty much everything I could find on the internet (though most of the 
threads I found were never resolved).
Tried ipa-cert-fix.
Tried ipa-restoring a backup in a new container, same problem occurs.

My guess is that an upgrade years back did break the certificate auto-renewal 
and went undetected, and now everything is expired it's failing.
 
If you have any ideas of what to check/try I would be very grateful as I am 
losing my sanity here.
Also, I am a bit scared of breaking what is currently working (ldap+sssd) and 
critical to our operations, so if anything can be tested on a copy of the data 
in a container that would be great. 

Thanks!
--
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