Graphenium v0.4.1: Incremental rebuild fixes

Graphenium v0.4.1

Patch release fixing two incremental rebuild bugs.

Fixed

• Critical data corruption in incremental rebuilds: replace_file_extraction now calls rebuild_id_index() after batch-removing stale nodes. Without this, petgraph swap-remove shifts node indices, silently corrupting id_index lookups during watch-mode rebuilds.

• Disconnected manifest invalidation: try_incremental now loads the manifest and uses invalidation_set() to include downstream importers in the re-extraction set, so cross-file resolution stays current during watch-mode builds.

Upgrade

cargo install --path .
gm run . --no-semantic --no-viz