refactor: extract main window registry and context ownership

[teamleaderleo]

Summary

Give main-window state explicit ownership instead of keeping the registry and model nested inside AppDelegate.

MainWindowRegistry owns identity indexing and lifecycle mutation. CmuxMainWindowContext is the independent model type (with the existing MainWindowContext compatibility alias). Test-only window mutations now use the same registry path, preserving production side effects and preventing the test seam from drifting.

Validation

• swiftc -D DEBUG -parse over the changed Swift sources
• scripts/check-pbxproj.sh
• git diff --check

A full Xcode build remains blocked in this checkout because vendor/bonsplit/Package.swift is not present.

[teamleaderleo]

Keeping the branch as implementation history; upstream delivery will be rebased onto manaflow-ai/cmux:main as part of a foundations slice.