OpenCode ships override command files under .opencode/commands/ that
shadow the generic commands/*.md sources. The manifest install plan
recorded both writes against the same destination, so `ecc doctor`
reported perpetual drift for the 29 shadowed command files and `ecc
repair` "fixed" that phantom drift by copying the generic source over
the correct override, corrupting the installed command while never
clearing the warning.
Dedupe copy-file operations by destination in createManifestInstallPlan,
keeping the last writer to match the sequential apply order. install,
repair, and doctor all consume this one builder, so a fresh install is
clean and a single repair rewrites drifted state green.
Fixes#2414
