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Added Claude Science 0.1.25 compatibility for updater runtimes, new-session control, authority trees, health checks, managed reattach, and stop/recovery identity.
Replaced whole-tree Science authority backups with a selective snapshot of credentials, organizations, MCP state, and SSH bridge metadata. Conda, Runtime, seed assets, R libraries, and sandbox bind sources remain opaque and are never traversed or copied, removing the multi-gigabyte cold-start snapshot path.
Split profile selection from runtime application: Set active now saves the local choice only, while Start is the single guarded transaction that validates, applies, starts, and opens Science.
Preserved selected-versus-applied truth across profile edits, preset sync, key clearing, deletion, rollback, and interrupted runtime operations.
Hardened managed Science and Gateway adoption against stale receipts, PID reuse, unproven restart candidates, late SSH failures, and incomplete authority recovery.