MCP servers that connect after the agent's one-time tool snapshot were
invisible for the whole session. Two root causes, fixed together:
1. The startup discovery wait was a flat 0.75s. HTTP/OAuth servers
commonly take 2-6s on a cold connect, so they missed the window and
their tools never entered the agent's snapshot. `thread.join(timeout)`
already returns the instant discovery completes, so raising the bound
costs ~0s for the common case (no MCP / fast servers) and only ever
blocks for a genuinely-pending server, capped so a dead server can't
freeze startup. The bound is now configurable via
`mcp_discovery_timeout` (config.yaml, default 5.0s).
2. Three call sites duplicated the agent tool-snapshot rebuild (the TUI
`reload.mcp` RPC, the gateway reload, and the TUI late-binding refresh
thread), and the late-refresh detected changes by tool COUNT — missing
an equal-size add/remove swap. Consolidated into one shared
`tools.mcp_tool.refresh_agent_mcp_tools(agent)` helper that diffs by
tool NAME, mutates the agent under a lock (thread-safe), and respects
the agent's own enabled/disabled toolsets.
The late-binding refresh keeps its pre-first-turn cache-safety guard:
it never rebuilds the tool list once a turn has started, so the cached
prompt prefix is never invalidated mid-conversation.
Tests: new tests/tools/test_refresh_agent_mcp_tools.py covers the
name-based diff, in-place mutation, agent-scoped filtering, thread
safety, and the config-driven discovery bound (incl. instant-return
when nothing is pending). 75 passed across the touched areas.
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