Improvements in IndexManager

[spoenemann]

• Don't remove the reference to the AstNode
• remove takes a single URI for consistency with other services
• Renamed protected properties for more clarity

[spoenemann]

Some context about deleting the node property in AstNodeDescriptions:

• We did that in the initial version of the IndexManager out of fear that such a reference could become outdated. But we're clearing the index anyway when a document needs to be reindexed, so it shouldn't be a problem in practice.
• We also had in mind that one might want to unload a document from memory to reduce the overall memory consumption of a workspace. But we never tried that and so far we haven't seen the need for it, so we should leave that topic for later (seeing a real example where unloading is necessary). Enabling such unloading will require more work, anyway, because linking is currently synchronous, so we can't load documents during linking.
• Serializing the index is also a topic, but that can be done with explicit IndexManager methods to be added in a future version.