docs: update paths for claude-plugin subdirectory structure (GH#985) (#1007)

Update documentation and scripts to reflect the plugin move from
root level to claude-plugin/ subdirectory:

- Fix command links in docs/DAEMON.md, docs/SYNC.md, examples/
- Update plugin.json path references in RELEASING.md, AGENT_INSTRUCTIONS.md
- Update scripts/bump-version.sh and scripts/check-versions.sh
- Update skill documentation paths in claude-plugin/skills/beads/

The marketplace.json correctly stays at .claude-plugin/ (root level)
while plugin.json moved to claude-plugin/.claude-plugin/.

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

examples/protected-branch/README.md

@@ -278,4 +278,4 @@ jobs:
 
 - [docs/PROTECTED_BRANCHES.md](../../docs/PROTECTED_BRANCHES.md) - Complete guide
 - [AGENTS.md](../../AGENTS.md) - Agent integration instructions
-- [commands/sync.md](../../commands/sync.md) - `bd sync` command reference
+- [commands/sync.md](../../claude-plugin/commands/sync.md) - `bd sync` command reference