analyzer: Do not create an unmanaged project for a single root directory

So far, if the directory structure was like

root-dir
 |
 +-.git
 |
 +-project-dir

still an unmanaged project would have been created because no definition
file is in the root directory, and the project directory is regarded as an
unmanaged "file", even though there are not really any unmanaged files in
the root.

Fix this by a introducing a check that removes all managed paths (or
ignored files) from all files in the root.

Signed-off-by: Sebastian Schuberth <sebastian.schuberth@bosch.io>

analyzer/src/main/kotlin/Analyzer.kt

@@ -35,6 +35,7 @@ import org.ossreviewtoolkit.model.Repository
 import org.ossreviewtoolkit.model.VcsInfo
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
+import org.ossreviewtoolkit.spdx.VCS_DIRECTORIES
 import org.ossreviewtoolkit.utils.CommandLineTool
 import org.ossreviewtoolkit.utils.Environment
 import org.ossreviewtoolkit.utils.log
@@ -72,11 +73,14 @@ class Analyzer(private val config: AnalyzerConfiguration) {
             Pair(manager, mappedFiles).takeIf { mappedFiles.isNotEmpty() }
         }.toMap(mutableMapOf())
 
-        val hasDefinitionFileInRootDirectory = managedFiles.values.flatten().any {
-            it.parentFile.absoluteFile == absoluteProjectPath
+        // Check whether there are unmanaged files (because of deactivated, unsupported, or non-present package
+        // managers) which we need to attach to an artificial "unmanaged" project.
+        val managedDirs = managedFiles.values.flatten().mapNotNull { it.parentFile }
+        val hasOnlyManagedDirs = absoluteProjectPath in managedDirs || absoluteProjectPath.listFiles().all {
+            it in managedDirs || it.name in VCS_DIRECTORIES
         }
 
-        if (factoryFiles.isEmpty() || !hasDefinitionFileInRootDirectory) {
+        if (!hasOnlyManagedDirs) {
             Unmanaged.Factory().create(absoluteProjectPath, config, repositoryConfiguration).let {
                 managedFiles[it] = listOf(absoluteProjectPath)
             }