Rather than using the optional, we now directly use `File.Index` which
can already represent an unknown file due to its `.null` value. This
means we do not pay for the memory cost.

This type of index is now used for:
- SymbolLoc
- Key of the functions map
- InitFunc

Now we can simply pass things like atom.file, object.file, loc.file etc
whenever we need to access its representing object file which makes it
a lot easier.