Mixed physical/logical locations in type checker messages

[sungshik]

Describe the bug

Some messages produced by the type checker have logical locations; some have physical locations.

To Reproduce

1. Set a breakpoint on the first line of method translateCheckResults in RascalLanguageServices.java. This function processes the messages produced by the type checker.
2. Launch a VS Code instance with the Rascal extension using the "Run Extension" launch configuration
3. Open a test workspace and run mvn clean
4. Create the following modules:

   // A.rsc
   module A
   import B;
   str x = y;
   
   // B.rsc
   module B
   public str y = "foo";
   public int z = false;

5. Trigger the type checker. The breakpoint will be hit. Inspect variable messages. It will show two messages with a physical location.
6. Add a space somewhere and trigger the type checker again. The breakpoint will be hit. Inspect variable messages. It will show two messages with a physical location and one message with a logical location.

[rodinaarssen]

The language server logs (on trace level) also show mixed locations (ultimately) coming from the type checker, for instance when messages on standard library modules (with a logical location) are dropped