Normalize doesn't properly expand new & improved macros with tokens

Saw this when trying to expand out my jbrowse tool to figure out why a filter wasn't working:

```


...
```

It's even worse on my jbrowse tool which uses multiply nested macros with yields + tokens, meaning figuring out the whole hierarchy for something like this is a nightmare:

```


Linear scaling
Logarithmic scaling



@AUTOMATIC_LABEL@
@MANUAL_LABEL@









Opacity (high scores = 1.0 opacity)
Brewer Color Schemes




@AUTOMATIC_LABEL@
@MANUAL_LABEL@

```

Start by locating Planemo's normalize entry point and the macro expansion logic used for tool XML. Trace how nested macros, yields, and tokens are handled for the examples in the issue. Done means normalization expands the shown macros correctly without leaving incorrect or unresolved token values.

Written by the indexing model from the issue text.