Warehouse connection registry is shared across projects served by one process #1566

Description

The warehouse connection registry (packages/opencode/src/altimate/native/connections/registry.ts) is process-global, but one server process serves several project directories (each request carries its own Instance.directory). As a result:

• The first project to load decides the connections for every project: project B sees project A's project-local .altimate-code/connections.json entries, and B's own file is ignored.
• Two projects that use the same connection name share one cached connector and one SSH tunnel. Reloading or removing in one project closes the other project's connector or tunnel.

#1559 stopped an empty-registry re-read from loading another project's file into the shared registry, but the registry itself is still shared.

Expected

Registry state (configs, connectors, in-flight connects, SSH tunnels) is kept per project directory. The global file and ALTIMATE_CODE_CONN_* env vars stay shared sources, merged into each project's state. A populated registry is still never replaced automatically.

Steps to reproduce

1. Run one server and open two projects, A and B, each with its own .altimate-code/connections.json.
2. List warehouses in A, then in B.
3. B lists A's connections.