Fix #274: Add automatic .beads/.gitignore upgrade (#300)

* Fix #274: Add automatic .beads/.gitignore upgrade

Implements three mechanisms to ensure users get updated gitignore:

1. bd doctor --fix: Manually upgrade gitignore
2. Daemon auto-upgrade: Upgrades on startup if outdated
3. bd init idempotent: Safe to re-run, always updates gitignore

The gitignore template now lives in cmd/bd/doctor/gitignore.go
for consistent updates across all three mechanisms.

Fixes: #274

* Remove test binary

Amp-Thread-ID: https://ampcode.com/threads/T-7042cfcc-ac97-43d7-a40f-3fa1bb4e1c2b
Co-authored-by: Amp <amp@ampcode.com>

* Fix critical issues: remove merge artifact and apply gitignore template

- Remove .beads/beads.left.jsonl (merge artifact that shouldn't be committed)
- Apply new gitignore template to .beads/.gitignore (was missing patterns)

Amp-Thread-ID: https://ampcode.com/threads/T-7042cfcc-ac97-43d7-a40f-3fa1bb4e1c2b
Co-authored-by: Amp <amp@ampcode.com>

* bd sync: 2025-11-12 11:09:30

* Retrigger CI

Amp-Thread-ID: https://ampcode.com/threads/T-8d532264-6d5e-4b68-88e9-e4511851b64a
Co-authored-by: Amp <amp@ampcode.com>

* Fix duplicate DoctorCheck type definition

* Trigger CI after fixing type conflict

Amp-Thread-ID: https://ampcode.com/threads/T-8d532264-6d5e-4b68-88e9-e4511851b64a
Co-authored-by: Amp <amp@ampcode.com>

---------

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

.beads/.gitignore

@@ -1,5 +1,6 @@
 # SQLite databases
 *.db
+*.db?*
 *.db-journal
 *.db-wal
 *.db-shm
@@ -14,11 +15,15 @@ bd.sock
 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)
-!*.jsonl
+!issues.jsonl
 !metadata.json
 !config.json
-
-# 3-way merge snapshot files (local-only, for deletion tracking)
-beads.base.jsonl
-beads.left.jsonl