Fix bd-in7q: prevent migrate-tombstones from corrupting deletions manifest (#554)

Root cause: bd doctor hydrate was re-adding migrated tombstones to the
deletions manifest because getCurrentJSONLIDs() included all issues,
including tombstones. When compared against git history, tombstones
appeared as 'deleted' and were incorrectly added to the manifest as new
deletions, corrupting the database on next sync.

Fix: Skip tombstone-status issues in getCurrentJSONLIDs() so they don't
participate in deletion detection. Tombstones represent already-recorded
deletions/migrations and shouldn't be treated as active issues.

Changes:
- cmd/bd/doctor/fix/deletions.go: Skip tombstones in getCurrentJSONLIDs()
- cmd/bd/doctor/fix/deletions_test.go: New tests for tombstone skipping
- cmd/bd/migrate_tombstones_test.go: Test that tombstones are valid

This fixes the bug where 'bd migrate-tombstones' followed by 'bd sync'
would add thousands of deletion records with author 'bd-doctor-hydrate'

.beads/.gitignore

@@ -1,20 +1,32 @@
-# Ignore all .beads/ contents by default (local workspace files)
-# Only files explicitly whitelisted below will be tracked in git
-*
+# SQLite databases
+*.db
+*.db?*
+*.db-journal
+*.db-wal
+*.db-shm
 
-# === Files tracked in git (shared across clones) ===
+# Daemon runtime files
+daemon.lock
+daemon.log
+daemon.pid
+bd.sock
 
-# This gitignore file itself
-!.gitignore
+# Local version tracking (prevents upgrade notification spam after git ops)
+.local_version
 
-# Issue data in JSONL format (the main data file)
+# Legacy database files
+db.sqlite
+bd.db
+
+# Merge artifacts (temporary files from 3-way merge)
+beads.base.jsonl
+beads.base.meta.json
+beads.left.jsonl
+beads.left.meta.json
+beads.right.jsonl
+beads.right.meta.json
+
+# Keep JSONL exports and config (source of truth for git)
 !issues.jsonl
-
-# Repository metadata (database name, JSONL filename)
 !metadata.json
-
-# Configuration template (sync branch, integrations)
-!config.yaml
-
-# Documentation for contributors
-!README.md
+!config.json

.beads/deletions.jsonl.migrated

@@ -0,0 +1,27 @@
+{"id":"bd-3pd","ts":"2025-12-02T05:05:53.732197Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-ksc","ts":"2025-12-02T05:05:53.742343Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-360","ts":"2025-12-02T05:05:53.74642Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.1","ts":"2025-12-14T06:42:56.65452Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.6","ts":"2025-12-14T06:42:56.660775Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.8","ts":"2025-12-14T06:42:56.66501Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.9","ts":"2025-12-14T06:42:56.669731Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.10","ts":"2025-12-14T06:42:56.674952Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.12","ts":"2025-12-14T06:42:56.678754Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.13","ts":"2025-12-14T06:42:56.682961Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.1","ts":"2025-12-14T06:42:56.686774Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.2","ts":"2025-12-14T06:42:56.690962Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.3","ts":"2025-12-14T06:42:56.694789Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.4","ts":"2025-12-14T06:42:56.698915Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.5","ts":"2025-12-14T06:42:56.702767Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.1","ts":"2025-12-14T06:43:28.945078Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.6","ts":"2025-12-14T06:43:28.951574Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.8","ts":"2025-12-14T06:43:28.956558Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.9","ts":"2025-12-14T06:43:28.961447Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.10","ts":"2025-12-14T06:43:28.96553Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.12","ts":"2025-12-14T06:43:28.969449Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cb64c226.13","ts":"2025-12-14T06:43:28.973591Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.1","ts":"2025-12-14T06:43:28.977362Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.2","ts":"2025-12-14T06:43:28.981423Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.3","ts":"2025-12-14T06:43:28.985436Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.4","ts":"2025-12-14T06:43:28.989612Z","by":"stevey","reason":"batch delete"}
+{"id":"bd-cbed9619.5","ts":"2025-12-14T06:43:28.993408Z","by":"stevey","reason":"batch delete"}

.beads/metadata.json

@@ -2,4 +2,4 @@
   "database": "beads.db",
   "jsonl_export": "issues.jsonl",
   "last_bd_version": "0.27.2"
-}
+}