Gotcha. We're optimizing for the same scenarios, may be worth a look at our implementation in case transferable to yours. See:
#1 - the "autosync" and GitHub integrations do exactly this.
#2 - The app auto-instals skills/MCP server configs for a few harnesses
#4 - We embedded agentic-search capabilities via the MCP server (e.g. we virtualize 'ls' and 'cat' so we can enrich it for the agent for better hierchical navigation).