## Why
Recent MCP runtime overlay changes replace same-name configured server
entries with compatibility or extension-provided configs. Those
replacement configs default to enabled, so an MCP server explicitly
configured with `enabled = false` could be initialized anyway.
The connection manager still filters disabled servers correctly, but the
configured disabled state was lost before initialization reached that
filter.
## What changed
- Remember MCP servers that are disabled in the configured view before
applying runtime fallbacks and extension overlays.
- Restore `enabled = false` for those servers after overlays, while
leaving all other overlay fields and `Remove` precedence unchanged.
- Add focused extension-backed regression coverage for a disabled
`codex_apps` server.
## Testing
- `just fmt`
- `just test -p codex-mcp-extension`
- `just fix -p codex-core`
- `just fix -p codex-mcp-extension`
The full workspace `just test` suite was not run.
