feat: auto-clean deprecated config fields on startup (#384)

* feat: auto-clean deprecated config fields on startup with backup

On startup, MCPProxy now removes deprecated config keys (top_k, enable_tray,
features) and creates a .bak backup of the original file before modifying it.
Telemetry showed 100% of doctor runs failing this check — this eliminates the
issue automatically instead of just warning.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: skip Unix-specific permission tests on Windows

The PreservesFilePermissions and ReadOnlyDir tests rely on Unix chmod
semantics that don't apply on Windows.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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Co-authored-by: Claude Code <noreply@anthropic.com>