[DevTask] Update serialisation methods

### Current

- `serialize` methods in Litegraph do not perform serialisation; they return an object that may be serialised
- In many cases, properties are simply copied to a new object, retaining collection refs
- In newer usage, many objects are shallow-cloned
- The intent is that the results from these functions are used exclusively for actions such as serialisation by the caller
- This is an ongoing cause of bugs due to (understandable) confusion around what these functions actually do

### Possible solutions

1. Shallow clone everything
- Performance impact on larger graphs
1. Actually serialise
- Strings cannot be easily modified downstream before writing to file
1. ...

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