chores(analyzer): Do not throw exception if duplicate packages

When duplicate packages or projects are found in the dependency tree, print a
warning instead of throwing an exception and inteerrupting the scan.
Duplicate packages may arise when the same package is imported twice, in these
cases the dependency tree will be completed as the package is imported at
least once.

Signed-off-by: Stefano Bennati <stefano.bennati@here.com>

analyzer/src/main/kotlin/AnalyzerResultBuilder.kt

@@ -19,6 +19,8 @@
 
 package org.ossreviewtoolkit.analyzer
 
+import org.apache.logging.log4j.kotlin.logger
+
 import org.ossreviewtoolkit.model.AnalyzerResult
 import org.ossreviewtoolkit.model.DependencyGraph
 import org.ossreviewtoolkit.model.DependencyGraphNavigator
@@ -41,9 +43,23 @@ class AnalyzerResultBuilder {
 
     fun build(excludes: Excludes = Excludes.EMPTY): AnalyzerResult {
         val duplicates = (projects.map { it.toPackage() } + packages).getDuplicates { it.id }
-        require(duplicates.isEmpty()) {
-            "Unable to create the AnalyzerResult as it contains packages and projects with the same ids: " +
-                duplicates.values
+        if (duplicates.isNotEmpty()) {
+            logger.warn {
+                "AnalyzerResult contains packages and projects with the same ids: ${duplicates.values}"
+            }
+            // Log duplicates as issues
+            for ((key, items) in duplicates) {
+                val issue = createAndLogIssue(
+                    source = "analyzer",
+                    message = "AnalyzerResult contains packages and projects with the same ids: ${items}"
+                )
+
+                val existingIssues = issues.getOrDefault(key, emptyList())
+                issues[key] = existingIssues + issue
+            }
+            // Remove duplicates from packages, to avoid side effects by having duplicate entries in the dependency tree
+            packages.removeAll { it.id in duplicates.keys.toSet() }
+
         }
 
         return AnalyzerResult(projects, packages, issues, dependencyGraphs)