docs: update beads.jsonl references to issues.jsonl

Fixes GH#409 - Documentation inconsistently referred to beads.jsonl
as the canonical filename when issues.jsonl has been the default
since v0.25.1 (bd-6xd).

Updated files:
- docs/ARCHITECTURE.md
- docs/CLI_REFERENCE.md
- docs/PROTECTED_BRANCHES.md
- docs/ADVANCED.md
- docs/GIT_INTEGRATION.md
- docs/MULTI_REPO_AGENTS.md
- docs/MULTI_REPO_MIGRATION.md
- docs/TROUBLESHOOTING.md
- examples/*/README.md
- skills/beads/references/CLI_REFERENCE.md

Note: beads.jsonl is still supported for backward compatibility.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

examples/protected-branch/README.md

@@ -176,11 +176,11 @@ my-project/
 │   ├── beads-worktrees/       # Hidden worktree directory
 │   │   └── beads-metadata/    # Lightweight checkout of sync branch
 │   │       └── .beads/
-│   │           └── beads.jsonl
+│   │           └── issues.jsonl
 │   └── ...
 ├── .beads/                    # Main beads directory (in your workspace)
 │   ├── beads.db               # SQLite database
-│   ├── beads.jsonl            # JSONL export
+│   ├── issues.jsonl            # JSONL export
 │   └── bd.sock                # Daemon socket (if running)
 ├── src/                       # Your application code
 │   └── ...
@@ -209,7 +209,7 @@ my-project/
 
 ### Troubleshooting
 
-**"Merge conflicts in beads.jsonl"**
+**"Merge conflicts in issues.jsonl"**
 
 JSONL is append-only and line-based, so conflicts are rare. If they occur:
 1. Both versions are usually valid - keep both lines