Consider corner cases in namespace manipulation for flattening

[bugarela]

From https://github.com/informalsystems/quint/pull/1109#discussion_r1298194884

I think the solution here is to change the importedFrom field to a list, keep track of the path of imports there, get rid of namespaces, and then find out the namespaces for a definition from the list of importedFrom field.

An example (and perhaps the only) scenario where we need the startsWith check is:

1. We have a qualified instance
2. The namespace for the instance is then myModule::A1
3. The name for some definition referencing the instance is A1::foo
4. When we add namespaces ['A1', 'myModule'] to A1::foo, I'd like it[^1] to become myModule::A1::foo.

Hopefully this will be trivial to solve when everything else is in place and I can test the interaction of changes in namespace manipulation and flattening on our set of examples.

[^1]: I'd like it in the sense that we probably don't need to, but it is more cognitively consistent and easier to explain if it behaves like this.