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/team-workflow/README.md

@@ -244,20 +244,20 @@ Hash-based IDs prevent most conflicts. If conflicts occur:
 ```bash
 # During git pull/merge
 git pull origin beads-metadata
-# CONFLICT in .beads/beads.jsonl
+# CONFLICT in .beads/issues.jsonl
 
 # Option 1: Accept remote
-git checkout --theirs .beads/beads.jsonl
-bd import -i .beads/beads.jsonl
+git checkout --theirs .beads/issues.jsonl
+bd import -i .beads/issues.jsonl
 
 # Option 2: Accept local
-git checkout --ours .beads/beads.jsonl
-bd import -i .beads/beads.jsonl
+git checkout --ours .beads/issues.jsonl
+bd import -i .beads/issues.jsonl
 
 # Option 3: Use beads-merge tool (recommended)
 # See docs/GIT_INTEGRATION.md for merge conflict resolution
 
-git add .beads/beads.jsonl
+git add .beads/issues.jsonl
 git commit
 ```
 
@@ -299,7 +299,7 @@ git commit
 
 ### Q: How do team members see each other's issues?
 
-A: Issues are stored in `.beads/beads.jsonl` which is version-controlled. Pull from git to sync.
+A: Issues are stored in `.beads/issues.jsonl` which is version-controlled. Pull from git to sync.
 
 ```bash
 git pull
@@ -372,9 +372,9 @@ bd daemon start --auto-commit --auto-push
 Use beads-merge or resolve manually (see [GIT_INTEGRATION.md](../../docs/GIT_INTEGRATION.md)):
 
 ```bash
-git checkout --theirs .beads/beads.jsonl
-bd import -i .beads/beads.jsonl
-git add .beads/beads.jsonl
+git checkout --theirs .beads/issues.jsonl
+bd import -i .beads/issues.jsonl
+git add .beads/issues.jsonl
 git commit
 ```