Only store references to one linker script in a resources object.

Projects have only ever made use of one linker script per compiler.
However, the tools would store references to multiple linker scripts in
a project and select one in a non-deterministic way. Now we clear out
any existing linker script when we add a new one to a project. This way,
the last added linker script is always used.

tools/resources/__init__.py

@@ -269,6 +269,10 @@ class Resources(object):
         if file_type:
             if sep != self._sep:
                 file_name = file_name.replace(sep, self._sep)
+            # Mbed OS projects only use one linker script at a time, so remove
+            # any existing linker script when adding a new one
+            if file_type == FileType.LD_SCRIPT:
+                self._file_refs[file_type].clear()
             self._file_refs[file_type].add(FileRef(file_name, file_path))
 
     def _include_file(self, ref):