Retired plugin nodes are pruned on update

When a plugin's source repository deletes a node — a NodeType, a document, an agent — updating the installed plugin now removes that node from the mesh instead of leaving an orphaned copy behind forever. Previously this only happened on a narrow "incremental update" path; a full re-install (which also runs whenever a plugin changes shared source code) silently kept every node the repo had already retired. A left-behind NodeType with no source left to compile against could later fail to rebuild and delay the affected instances from starting up. Updates are now consistent: whatever the repo no longer ships is removed from the installed partition.