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>

docs/DAEMON.md

@@ -592,4 +592,4 @@ bd daemons killall
 - [AGENTS.md](../AGENTS.md) - Main agent workflow guide
 - [EXCLUSIVE_LOCK.md](EXCLUSIVE_LOCK.md) - External tool integration
 - [GIT_INTEGRATION.md](GIT_INTEGRATION.md) - Git workflow and merge strategies
-- [commands/daemons.md](../commands/daemons.md) - Daemon command reference
+- [commands/daemons.md](../claude-plugin/commands/daemons.md) - Daemon command reference