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/contributor-workflow/README.md

@@ -58,7 +58,7 @@ When you create issues as a contributor:
 bd create "Fix authentication bug" -p 1
 ```
 
-Beads automatically routes this to your planning repo (`~/.beads-planning/.beads/beads.jsonl`), not the current repo.
+Beads automatically routes this to your planning repo (`~/.beads-planning/.beads/issues.jsonl`), not the current repo.
 
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