Fix entire clean logging leak and branch deletion with packed refs

[khaong]

Summary

• Logging fix: entire clean leaked structured logs (e.g. INFO deleted orphaned shadow branch...) to stderr instead of .entire/logs/entire.log because logging.Init() was never called. Added initialization in runClean().
• Branch deletion fix: entire clean --force reported shadow branches as deleted but they persisted. Root cause: go-git v5's RemoveReference() doesn't work with packed refs (.git/packed-refs) or worktree contexts. Replaced all 7 non-test RemoveReference call sites with git branch -D via CLI, consistent with the existing HardResetWithProtection() workaround pattern.

Test plan

• mise run fmt — passes
• mise run lint — passes (0 issues)
• mise run test:ci — all unit + integration tests pass
• Manual test: create a repo with packed refs + shadow branches, run entire clean -f, verify branches are actually gone with git branch -l 'entire/*'

🤖 Generated with Claude Code

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Note

Medium Risk
Switching branch deletion to git subprocesses changes behavior and error handling across multiple session/cleanup paths and depends on a working git executable/workdir; mistakes could leave stale shadow branches or delete the wrong ref.

Overview
Fixes entire clean to initialize structured logging so cleanup audit logs are written to .entire/logs/ instead of leaking to stderr.

Replaces shadow-branch deletion across cleanup/session flows from go-git RemoveReference to a new strategy.DeleteBranchCLI (backed by git show-ref + git branch -D) to reliably delete branches when refs are packed or in worktree contexts; updates related code paths (checkpoint.GitStore.DeleteShadowBranch, doctor discard, manual-commit reset/migration/condensation) and adjusts tests to validate deletion via git CLI rather than go-git ref reads.

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[Copilot]

Pull request overview

This PR addresses two operational issues in the Entire CLI cleanup path: (1) structured logs from entire clean appearing on stderr due to missing logging initialization, and (2) shadow branch deletions not persisting when refs are packed or in worktree contexts by switching branch deletion from go-git to git branch -D.

Changes:

• Initialize structured logging in runClean() so cleanup logs go to .entire/logs/entire.log instead of stderr.
• Replace go-git RemoveReference() branch deletion with git branch -D via a shared DeleteBranchCLI helper and update call sites.
• Adjust cleanup tests to verify branch deletion via git CLI (avoids go-git ref cache/staleness issues).

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
cmd/entire/cli/clean.go	Initializes logging for entire clean so structured cleanup logs are routed to the log file.
cmd/entire/cli/sessions_fix.go	Switches stuck-session shadow branch cleanup to use CLI-based branch deletion.
cmd/entire/cli/strategy/common.go	Adds DeleteBranchCLI() helper using git branch -D.
cmd/entire/cli/strategy/cleanup.go	Uses DeleteBranchCLI() for deleting orphaned shadow branches.
cmd/entire/cli/strategy/clean_test.go	Verifies branch deletion using git CLI for accuracy vs go-git ref visibility.
cmd/entire/cli/strategy/manual_commit_git.go	Updates shadow-branch deletion helper to use CLI deletion and treat “not found” as idempotent.
cmd/entire/cli/strategy/manual_commit_condensation.go	Updates shadow-branch cleanup to delete via CLI and treat “not found” as non-fatal.
cmd/entire/cli/strategy/manual_commit_migration.go	Deletes old shadow branches via CLI during migration (packed refs/worktrees workaround).
cmd/entire/cli/strategy/manual_commit_reset.go	Deletes shadow branches via CLI during reset.
cmd/entire/cli/checkpoint/temporary.go	Switches checkpoint store shadow-branch deletion to git branch -D for packed refs/worktrees reliability.

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.

[cursor]

Cursor Bugbot has reviewed your changes and found 1 potential issue.

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