To reproduce:
1. Download the project "CreateAssetMenuScriptableObject.zip" and delete it's Library folder if present
2. Open the addressed project
3. Observe the console

Result: APIUpdater throws multiple StackOverflowException errors

Reproduced in: 2019.3.0a3
Not reproduced in: 2017.4.25f1, 2018.4.1f1, 2019.1.3f1, 2019.2.0b2, 2019.3.0a2

Note1: does not reproduce when reimporting all the assets
Note2: full stack trace (message repeating ):

StackOverflowException: The requested operation caused a stack overflow.
System.Collections.Generic.List`1[T].System.Collections.Generic.IEnumerable<T>.GetEnumerator () (at <23c160f925be47d7a4fd083a3a62c920>:0)
UnityEditor.Scripting.APIUpdater.AssemblyDependencyGraph.HasDirectOrIndirectDependencyRecursive (UnityEditor.Scripting.APIUpdater.AssemblyDependencyGraph+DependencyEntry toBeLookedUp, System.Collections.Generic.IEnumerable`1[T] dependencies) (at C:/buildslave/unity/build/Editor/Mono/Scripting/APIUpdater/AssemblyDependencyGraph.cs:182)
UnityEditor.Scripting.APIUpdater.AssemblyDependencyGraph.HasDirectOrIndirectDependencyRecursive
C:/b<message truncated>

Note3: if Project folder is also deleted, each time upon loading a project there will also be PrecompiledAssemblyException errors

PrecompiledAssemblyException: Multiple precompiled assemblies with the same name Mono.Cecil.dll included for the current platform. Only one assembly with the same name is allowed per platform. Assembly paths: Assets/Mono.Cecil.dll, C:/Users/vaida/Downloads/CreateAssetMenuScriptableObject/CreateAssetMenuScriptableObject/Library/PackageCache/nuget.mono-cecil@0.1.5-preview/Mono.Cecil.dll
UnityEditor.Scripting.ScriptCompilation.EditorBuildRules.CreateTargetAssemblies (System.Collections.Generic.IEnumerable`1[T] customScriptAssemblies, System.Collections.Generic.IEnumerable`1[T] precompiledAssemblies) (at C:/buildslave/unity/build/Editor/Mono/Scripting/ScriptCompilation/EditorBuildRules.cs:275)
UnityEditor.Scripting.ScriptCompilation.EditorCompilation.UpdateCustomTargetAssemblies () (at C:/buildslave/unity/build/Editor/Mono/Scripting/ScriptCompilation/EditorCompilation.cs:722)
UnityEditor.Scripting.ScriptCompilation.EditorCompilation.SetAllCustomScriptAssemblyReferenceJsonsContents (System.String[] paths, System.String[] contents) (at C:/buildslave/unity/build/Editor/Mono/Scripting/ScriptCompilation/EditorCompilation.cs:869)
UnityEditor.Scripting.ScriptCompilation.EditorCompilationInterface.SetAllCustomScriptAssemblyReferenceJsons (System.String[] allAssemblyReferenceJsons, System.String[] allAssemblyReferenceJsonContents) (at C:/buildslave/unity/build/Editor/Mono/Scripting/ScriptCompilation/EditorCompilationInterface.cs:241)