Remove deprecated factories

The various factories (like [CollectionTypeAdapterFactory](https://github.com/eclipse-lsp4j/lsp4j/blob/ad99a3d77139351dbc00c2dacd388fe749652309/org.eclipse.lsp4j.jsonrpc/src/main/java/org/eclipse/lsp4j/jsonrpc/json/adapters/CollectionTypeAdapterFactory.java#L22)) seem to be easy decisions to remove