fix(autoimport): auto-correct deleted status to tombstone for JSONL compatibility (#1231)

* fix(autoimport): auto-correct deleted status to tombstone for JSONL compatibility (GH#1223)

This fix addresses the 'Stuck in sync diversion loop' issue where v0.48.0
encountered validation errors during JSONL import. The issue occurs when
JSONL files from older versions have issues with status='deleted' but the
current code expects status='tombstone' for deleted issues.

Changes:
- Add migration logic in parseJSONL to auto-correct 'deleted' status to 'tombstone'
- Ensure tombstones always have deleted_at timestamp set
- Add debug logging for both migration operations
- Prevents users from being stuck in sync divergence when upgrading

Fixes GH#1223: Stuck in sync diversion loop

* fix(autoimport): comprehensively fix corrupted deleted_at on non-tombstone issues (GH#1223)

The initial fix for GH#1223 only caught issues with status='deleted', but the real
data in the wild had issues with status='closed' (or other statuses) but also
had deleted_at set, which violates the validation rule.

Changes:
- Add broader migration logic: any non-tombstone issue with deleted_at should become tombstone
- Apply fix in all three JSONL parsing locations:
  - internal/autoimport/autoimport.go (parseJSONL for auto-import)
  - cmd/bd/import.go (import command)
  - cmd/bd/daemon_sync.go (daemon sync helper)
- Add comprehensive test case for corrupted closed issues with deleted_at
- Fixes the 'non-tombstone issues cannot have deleted_at timestamp' validation error
  during fresh bd init or import

Fixes GH#1223: Stuck in sync diversion loop

* Add merge driver comment to .gitattributes

* fix: properly clean up .gitattributes during bd admin reset

Fixes GH#1223 - Stuck in sync diversion loop

The removeGitattributesEntry() function was not properly cleaning up
beads-related entries from .gitattributes. It only removed lines
containing "merge=beads" but left behind:
- The comment line "# Use bd merge for beads JSONL files"
- Empty lines following removed entries

This caused .gitattributes to remain in a modified state after
bd admin reset --force, triggering sync divergence warning loop.

The fix now:
- Skips lines containing "merge=beads" (existing behavior)
- Skips beads-related comment lines
- Skips empty lines that follow removed beads entries
- Properly cleans up file so it's either empty (and gets deleted)
  or contains only non-beads content

---------

Co-authored-by: Amp <amp@example.com>

.beads/config.yaml

@@ -6,7 +6,7 @@
 # Issue prefix for this repository (used by bd init)
 # If not set, bd init will auto-detect from directory name
 # Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc.
-issue-prefix: "bd"
+# issue-prefix: ""
 
 # Use no-db mode: load from JSONL, no SQLite, write back after each command
 # When true, bd will use .beads/issues.jsonl as the source of truth
@@ -37,12 +37,20 @@ issue-prefix: "bd"
 # Debounce interval for auto-flush (can also use BEADS_FLUSH_DEBOUNCE)
 # flush-debounce: "5s"
 
-# Sync branch for multi-clone setups
-# When set, .beads changes are committed to this branch via worktree
-# instead of the current branch. This allows multiple clones to sync
-# beads data without polluting main branch commits.
-# Can also be set via BEADS_SYNC_BRANCH environment variable.
-sync-branch: "beads-metadata"
+# Git branch for beads commits (bd sync will commit to this branch)
+# IMPORTANT: Set this for team projects so all clones use the same sync branch.
+# This setting persists across clones (unlike database config which is gitignored).
+# Can also use BEADS_SYNC_BRANCH env var for local override.
+# If not set, bd sync will require you to run 'bd config set sync.branch <branch>'.
+sync-branch: "beads-sync"
+
+# Multi-repo configuration (experimental - bd-307)
+# Allows hydrating from multiple repositories and routing writes to the correct JSONL
+# repos:
+#   primary: "."  # Primary repo (where this database lives)
+#   additional:   # Additional repos to hydrate from (read-only)
+#     - ~/beads-planning  # Personal planning repo
+#     - ~/work-planning   # Work planning repo
 
 # Integration settings (access with 'bd config get/set')
 # These are stored in the database, not in this file: