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Nested BrainPalace projects are auto-excluded from the outer index. Any subfolder with its own .brainpalace/ is treated as a separately indexed project and pruned (whole subtree) from the outer project's discovery and file watching. Checked live on every walk/event, so deleting the nested .brainpalace/ lets the outer index pick the subtree back up.
brainpalace init --migrate-graph-store / --no-migrate-graph-store + an interactive prompt (default yes) to upgrade an already-initialized project from the legacy simple graph store to sqlite. The existing graph replays into sqlite on next start (JSON kept for rollback); non-interactive runs migrate only with the flag (or --yes).
Fixed
Graph status reported 0 entities at cold start. The lazy-initialized graph store now hydrates entity_count/relationship_count from the persisted graph_metadata.json sidecar, so brainpalace status reflects the on-disk graph size immediately after boot (data was never lost).
Re-init dropped interactive answers. On an already-initialized project, answering the git-history / summarize / embed prompts (or passing the flags) is now persisted — previously the existing-project branch ignored them. The result banner now reads the true session state from config.yaml.
Changed
brainpalace init prompt order: the graph-store upgrade is now asked with the other questions and shown as a row in the init will: preview before Proceed? (declining also cancels the upgrade). Mono-repo-root refusal happens before any prompt.