Removes the `files` field from the Wasm linker, storing the ZigObject
as its own field instead using a tagged union.

This removes a layer of indirection when accessing the ZigObject, and
untangles logic so that we can introduce a "pre-link" phase that
prepares the linker state to handle only incremental updates to the
ZigObject and then minimize logic inside flush().

Furthermore, don't make array elements store their own indexes, that's
always a waste.

Flattens some of the file system hierarchy and unifies variable names
for easier refactoring.

Introduces type safety for optional object indexes.