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fix(harness): preserve deferred base-tool activation when multi-agent tools register #516

Description

@zhnt

Regression: Coding bootstrap requests the seven base tools before their definitions are published. Multi-agent registration currently rebuilds requested activation from active_names only, dropping those deferred requests and leaving the root session with only the six collaboration tools. Scope: introduce an explicit additive activation operation, route dynamic multi-agent registration through it, preserve exact replacement for user/profile operations, and add deterministic startup-order and disablement regressions. Acceptance: after collaboration registration and base-tool publication, requested and active sets contain all expected tools; user-disabled tools remain disabled; provider-facing schemas match the logical active set.

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