Here is something I noticed that may be a clue. Maybe it will help.
I have three custom .phar files in the project. One of them works as expected, with Intellisense finding the classes and auto-complete, etc. The other two do not work and behave as I posted above. I inspected the .phar files to see if there was some error causing the issue but I could not find it. Also, Intellisense did work for all three of my custom .phar at some point. I am not sure when it stopped working. The application runs fine and has no problem with the .phar files and classes at runtime.
Thank you