indexAllArtifacts and ensureArtifactsIndexed previously called saveContextMetadata only once, after the entire indexing pass completed. When the underlying loop took longer than the MCP client's tool-call timeout, completed artifacts appeared unindexed because their state was never persisted, and partial progress was lost.
This patch saves the metadata snapshot after every successfully indexed artifact, so each artifact's success is durable as soon as the indexing for it returns. It also seeds the in-flight stateMap from the previously-loaded existingStates so that interrupted runs can preserve completed work for artifacts already finished, and uses that same original snapshot to identify orphan artifacts that need cleanup when the config has changed.
Backwards compatible: a successful full run produces exactly the same final on-disk state as before. The only behavioural difference is in the interrupted-mid-run case, where the new code retains more state instead of losing everything since the last full pass.
Tests: 3 new cases in tests/unit/context-artifacts-checkpoint.test.ts covering the checkpointing path during full indexing, preservation of earlier successes when a later artifact fails, and preservation of up-to-date states while re-indexing stale ones. Existing unit tests continue to pass unchanged.
Co-authored-by: jackblackjack chugarev@gmail.com
Aleksey Chugarev