Near as I can tell in my jooq/gradle/java17 setup on a mac11.6.2 a call to 
generatJooq is dropping all the java files, including the application files, 
then generating the database classes.  This is rather troubling.  First spotted 
on version 3.14, I’ve moved all my dependencies forward including vaadin 22 
(which is giving me a separate set of troubles)

Here’s my jooq/gradle block.
jooq {
  version = '3.15.+'
  edition = nu.studer.gradle.jooq.JooqEdition.OSS  // the default (can be 
omitted)
  dependencies {
    jooqGenerator 'org.postgresql:postgresql:42.2.14'
  }
  configurations {
    if (referenceDBname.contains("DBNAME_NOT_SET")) { 
      println("HEADS UP: you will need to configure the reference database: " + 
referenceDBname)
    }
    else {
      println("Generating jOOQ code from " + referenceDBname)
    }
    main {  // name of the jOOQ configuration
          generateSchemaSourceOnCompilation = ! referenceDBname == 
'DBNAME_NOT_SET'  // default (can be omitted)
          generationTool 
          {
        logging = org.jooq.meta.jaxb.Logging.INFO
        jdbc {
          driver = 'org.postgresql.Driver'
          url = String.format("jdbc:postgresql://%s:%s/%s", referenceDBhost, 
referenceDBport, referenceDBname)
          user = 'postgres'
          if (project.hasProperty("referenceDBpswd")) {
            password = referenceDBpswd
          }
          else {
            println "No dbpwd"
          }
        }
        generator {
          database {
            // forcedTypes {
            //   forcedType {
            //     userType = 'java.util.LocalDateTime'
            //     converter = 'com.skatr.tsn.util.DateTimeConverter'
            //     includeExpression = '.*timestamp.*'
            //   }
            // }
            name = 'org.jooq.meta.postgres.PostgresDatabase'
            schemaVersionProvider = 'select max(version::int) FROM 
public.flyway_schema_history'
            includeRoutines = true
            schemata {
              schema {
                inputSchema = 'public'
              }
              schema {
                inputSchema = 'suas'
              }
            }
          }
          generate {
            deprecated               = false
            fluentSetters            = true
            generatedAnnotation      = true
            generatedAnnotationType  = 'DETECT_FROM_JDK'
            globalRoutineReferences  = true
            immutablePojos           = false
            pojos                    = true
            records                  = true
            relations                = true
            routines                 = true
          }
          target {
            packageName = 'com.skatr.db.gen'
            directory = 'src/main/java'
          }
          strategy.name = 'org.jooq.codegen.DefaultGeneratorStrategy'
        }
      }
    }
  }
}

tasks.named('generateJooq').configure {
  // make jOOQ task participate in incremental builds (which is also a 
prerequisite for participating in build caching)
  allInputsDeclared = true
  // make jOOQ task participate in build caching
  outputs.cacheIf { true }
}

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