Investigate exceptions in jenkins startup log

Coming out of https://github.com/adoptium/infrastructure/issues/3636 we have quite a few exceptions, some of which are from missing config.xml on old directory.

Lots of warnings from missing files under build-scripts `WARNING c.c.h.p.folder.AbstractFolder#loadChildren: could not find file /home/jenkins/.jenkins/jobs`
```
build-scripts/jobs/jdk8u/config.xml
build-scripts-testing/jobs/jdk8u/config.xml
build-scripts-testing/jobs/jdk11u/config.xml
build-scripts/jobs/jdk11u/config.xml
build-scripts/jobs/jdk15u/config.xml
build-scripts/jobs/jdk16/config.xml
build-scripts/jobs/jdk/config.xml
build-scripts/jobs/jdk16u/config.xml
build-scripts-testing/jobs/jdk8u/config.xml
build-scripts-testing/jobs/jdk11u/config.xml
build-scripts/jobs/jdk8u/config.xml
build-scripts/jobs/jdk11u/config.xml
build-scripts/jobs/jdk15u/config.xml
build-scripts/jobs/jdk16/config.xml
build-scripts/jobs/jdk/config.xml
build-scripts/jobs/jdk16u/config.xml
```
Most of the others seem to be one of these (checkboxes added to indicate when they've been addressed)
- [ ] `Caused: java.io.IOException: Failed to persist /home/jenkins/.jenkins/jobs/build-scripts/jobs/jobs/jobs/jdk22/jobs/jdk22-linux-x64-temurin/builds/53/program.dat`
- [ ] `2024-07-02 08:39:09.247+0000 [id=3954088] WARNING hudson.model.Slave#reportLauncherCreateError: Issue with creating launcher for agent test-docker-ubuntu2404-s390x-2. The agent has not been fully initialized yetProbably there is a race condition with Agent reconnection or disconnection, check other log entries`
- [ ] `2024-07-02 08:41:20.164+0000 [id=3954052] SEVERE jenkins.model.Jenkins#_cleanUpPluginServletFilters: Failed to stop filters`
- [ ] `java.lang.IllegalStateException: Jenkins.instance is missing. Read the documentation of Jenkins.getInstanceOrNull to see what you are doing wrong.`
- [ ] Quite a few of these: `Caused by: java.lang.AssertionError: class hudson.security.csrf.DefaultCrumbIssuer is missing its descriptor`
- [ ] `2024-07-02 10:25:11.165+0000 [id=3661] INFO hudson.slaves.ChannelPinger$1#onDead: Ping failed. Terminating the channel test-docker-alpine314-x64-1.`

Start with the Jenkins startup log and the related issue 3636, then compare the warnings against /home/jenkins/.jenkins/jobs and the listed build-scripts/*/jobs/*/config.xml paths. Review each unchecked exception and agent warning to determine its cause and document the required remediation; done means the exceptions are explained and actionable follow-up is recorded.

Written by the indexing model from the issue text.