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>

AGENT_INSTRUCTIONS.md

@@ -343,7 +343,7 @@ git push origin main
 **Files updated automatically:**
 
 - `cmd/bd/version.go` - CLI version
-- `.claude-plugin/plugin.json` - Plugin version
+- `claude-plugin/.claude-plugin/plugin.json` - Plugin version
 - `.claude-plugin/marketplace.json` - Marketplace version
 - `integrations/beads-mcp/pyproject.toml` - MCP server version
 - `README.md` - Documentation version