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/git-hooks/README.md

@@ -129,11 +129,11 @@ This solves bd-my64: changes made between commit and push (or pending debounced
 After a git pull or merge, the hook runs:
 
 ```bash
-bd import -i .beads/beads.jsonl
+bd import -i .beads/issues.jsonl
 ```
 
 This ensures your local database reflects the merged state. The hook:
-- Only runs if `.beads/beads.jsonl` exists (also checks `issues.jsonl` for backward compat)
+- Only runs if `.beads/issues.jsonl` exists (also checks `issues.jsonl` for backward compat)
 - Imports any new issues or updates from the merge
 - Warns on failure but doesn't block the merge