When analyzing the attached application with a target of jakarta-ee rules are firing for classes that belong to known software artifacts.
If you look at this artifact in Maven Central
https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind/2.12.3 there are a number of files that have the .module* suffix.
This has been known to cause problems with the Nexus indexer resulting in gaps in the lucene index of known software artifacts.

There are 2 aspects to consider
1. Why the presence of .module* files is causing the gaps in the index
2. Is there a workaround way of adding the missing sha1 hash files to the lucene index