Track worktree path/root resolution fixes across bd commands

[osamu2001]

Summary

Track the small, reviewable fixes that make Beads behave consistently when commands are run from git worktrees.

The goal is to ensure that worktree execution resolves the shared Beads state from the main repository when appropriate, instead of assuming a local ./.beads or worktree-local repo root.

Background

A number of commands still have command-specific assumptions about:

• local ./.beads
• worktree root vs main repo root
• hooks/config/doctor checks using relative paths that only work in non-worktree repos

These PRs intentionally split the work into focused units so each behavior can be reviewed independently without bundling unrelated cleanup.

PRs in this tracking set

• fix: remove stale worktree guard in rename-prefix #3114 fix: remove stale worktree guard in rename-prefix - remove an outdated guard that blocked bd rename-prefix in worktrees
• fix: add worktree fallback to countExistingIssues #3115 fix: add worktree fallback to countExistingIssues - make bd init --force count issues via worktree-aware fallback
• fix: use FindBeadsDir for worktree-aware reset #3116 fix: use FindBeadsDir for worktree-aware reset - make bd reset resolve the shared Beads dir correctly
• fix: use worktree fallback in bootstrap path synthesis #3117 fix: use worktree fallback in bootstrap path synthesis - avoid creating stray .beads in worktrees during bootstrap
• fix: use main repo root for hooks path in worktrees #3118 fix: use main repo root for hooks path in worktrees - make hooks install/reset target the main repo root in worktrees
• fix: worktree-aware path resolution in config validate and preflight #3119 fix: worktree-aware path resolution in config validate and preflight - make config/preflight checks resolve Beads paths correctly in worktrees
• fix: use worktree-aware beads dir in doctor checks #3120 fix: use worktree-aware beads dir in doctor checks - make doctor checks use worktree-aware Beads dir resolution

Expected outcome

After these land, worktree usage should be more consistent across:

• bd init --force
• bd reset
• bd bootstrap
• bd hooks install
• bd config validate
• bd preflight
• bd doctor
• bd rename-prefix

Scope boundary

This issue is only for the targeted worktree path/root resolution fixes above.

It does not bundle larger design changes or unrelated cleanup. The split is intentional to keep review complexity low while preserving a shared review context.

[maphew]

All 7 PRs in this series have been reviewed and merged. Great work splitting these into focused, independently reviewable units — each with clean commit history and solid integration tests. Thanks for the thorough worktree support improvements, @osamu2001!

Merged:

• fix: remove stale worktree guard in rename-prefix #3114 rename-prefix guard removal
• fix: add worktree fallback to countExistingIssues #3115 countExistingIssues fallback
• fix: use FindBeadsDir for worktree-aware reset #3116 reset worktree-aware path (with minor dead-code cleanup)
• fix: use worktree fallback in bootstrap path synthesis #3117 bootstrap stray .beads prevention
• fix: use main repo root for hooks path in worktrees #3118 hooks main repo root (with IsWorktree guard simplification)
• fix: worktree-aware path resolution in config validate and preflight #3119 config/preflight path resolution
• fix: use worktree-aware beads dir in doctor checks #3120 doctor checks

Note: 13 more files still have hardcoded .beads paths that may need similar treatment — happy to review follow-up PRs.

[maphew]

Closing — all tracked worktree fixes have landed in main (PRs #3114–#3120, #3123, #3168, #3183) with tests for every affected command. The follow-up in #3183 covered the remaining runtime .beads fallbacks.