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

So far, if the directory structure was like

root
 |
 +-.git
 |
 +-project

still an unmanaged project would have been created because no definition
file is in the root, 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

@@ -40,6 +40,7 @@ import org.ossreviewtoolkit.model.VcsInfo
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.readValue
+import org.ossreviewtoolkit.spdx.VCS_DIRECTORIES
 import org.ossreviewtoolkit.utils.NamedThreadFactory
 import org.ossreviewtoolkit.utils.ORT_REPO_CONFIG_FILENAME
 import org.ossreviewtoolkit.utils.log
@@ -87,11 +88,14 @@ 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 (either because of an unsupported, deactivated or non-present package
+        // manager) which we need to attach to a "fake" unmanaged project.
+        val managedDirectories = managedFiles.values.flatten().mapNotNull { it.parentFile }
+        val unmanagedFiles = absoluteProjectPath.listFiles().filterNot {
+            it in managedDirectories || it.name in VCS_DIRECTORIES
         }
 
-        if (factoryFiles.isEmpty() || !hasDefinitionFileInRootDirectory) {
+        if (unmanagedFiles.isNotEmpty()) {
             Unmanaged.Factory().create(absoluteProjectPath, config, repositoryConfiguration).let {
                 managedFiles[it] = listOf(absoluteProjectPath)
             }