Fix gt-pvx auto-save committing deletions of tracked files

[justinstimatze]

Summary

• Both auto-save mechanisms (gt done safety net and checkpoint_dog) use git add -A which stages deletions of tracked files
• A polecat whose working tree has a missing tracked file (e.g. .beads/metadata.json) gets that deletion auto-committed, breaking infrastructure for subsequent sessions
• Fix: after git add -A, unstage all staged deletions via git diff --cached --name-only --diff-filter=D
• Also adds runtime dir exclusions to done.go (.beads/, .claude/, .runtime/, __pycache__/) matching checkpoint_dog's existing runtimeExcludeDirs

Fixes #3615

Changes

• internal/git/git.go — new StagedDeletions() method
• internal/cmd/done.go — add runtime dir exclusions + deletion unstaging
• internal/daemon/checkpoint_dog.go — add deletion unstaging after existing runtime dir exclusions

Design rationale

A safety-net auto-commit should preserve work (additions + modifications), never destroy it (deletions). Renames are unaffected — git detects them as R status, not D, even with content changes down to 75% similarity.

Test plan

• go build ./... passes
• go test ./internal/git/... passes
• go test ./internal/daemon/... passes
• Verified renames not caught by --diff-filter=D (tested at 100% and 75% similarity)
• Verified complete file replacement (0% similarity) correctly unstages deletion, preserving the new file
• go test ./internal/cmd/... has pre-existing compile error in compact_report_test.go (unrelated)