--skip-worktree is an index flag. GitWorktrees.snapshot staged into a fresh
empty temp index, which carried none of the real index's skip-worktree bits,
so add -A staged local on-disk content for files git status correctly hides
(e.g. .mcp.json). Copy the real index (resolved via git rev-parse --git-path
index, correct for linked worktrees) into the temp index before staging, so
add -A skips exactly what git status skips.
Dai Ha
2db7189067