5.3.6 is about making the normal working path stay normal. If a user installs or updates NEXO, opens Claude Code, runs nexo chat, and expects the managed shared-brain server to be there, the product should not depend on a stale config assumption to make that happen.
The real mismatch
NEXO already knew how to sync managed Claude Code settings. The problem was that current Claude Code builds read user-scoped MCP servers from ~/.claude.json, while NEXO still wrote the managed MCP server only to ~/.claude/settings.json. That left a bad daily-work outcome: the runtime itself could be fine, yet claude mcp and interactive sessions still missed the NEXO server.
What 5.3.6 changes
Managed client sync now writes the NEXO MCP server to ~/.claude.json as well, while still keeping Claude's managed settings file in sync for hooks and bootstrap. That means the runtime, the CLI, and Claude Code itself all point at the same managed server instead of drifting across two config surfaces.
Why this matters
Bootstrap bugs are trust bugs. If a user runs nexo update, restarts, and the shared brain disappears because the MCP server landed in the wrong config file, the product feels fragile even when the underlying runtime is solid. A patch release that restores the intended daily path is worth shipping quickly and clearly.
Other runtime hygiene in the same release
The patch also tightens a few nearby edges that affect operator trust: nexo schedule status now distinguishes still-running jobs from broken runs instead of flattening missing exit codes into failure; runtime script classification reads more of the actual packaged/core surface before calling something personal; retroactive learnings stop opening keyword-only false positives when a learning's declared applies_to scope does not match; and the final release-audit skill resolves repo roots more robustly across real operator layouts.
Upgrade
Open the 5.3.6 changelog section for the exact release note. For installed users, the intended path stays straightforward:
npm install -g nexo-brain@5.3.6nexo updatenexo doctor
Your data still lives in ~/.nexo. The runtime stays replaceable. What changes is that the managed Claude path now lands where Claude really looks for it.