#1153 ToolDef TypeMatcher.substitute now does proper deepcloning to prevent crashes

• Best to review per commit.
• End-user visible change:
  • ToolDef type checker: bugs have been fixed that could make the type checker crash or reject valid scripts. It concerns certain specific cases involving tool invocations with specifically typed arguments, or tools invoked by tool invocations with specifically-typed parameters or return types. Problems could previously occur if these types contain container types that have element types that are type references.
• Other changes:
  • I fixed another deepcloning issue. It is currently not end-user visible, I think.
  • I added an extra assertion, to fail early when type normalization results in null.

Addresses #1153 (closed)