fix: use root .gitignore instead of info/exclude for workspace cleanliness

[davidpoblador]

Summary

• .bare/info/exclude is shared across all linked worktrees, so patterns meant for the project root (.mise/, AGENTS.md, etc.) were also hiding those names inside worktrees
• Replaces the info/exclude approach with a wildcard .gitignore at the project root, which only affects the _workspace checkout
• Fixes .bare/ and main/ (and any dynamically-created worktree dirs) showing as untracked in git status at the project root

Test plan

• Scaffold fresh project (no remote): git status returns clean
• Scaffold with remote URL: git status returns clean
• Files inside linked worktrees are visible (not hidden by shared excludes)
• Dynamically-added worktrees don't appear as untracked at root

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