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>

scripts/check-versions.sh

@@ -43,8 +43,8 @@ check_version "integrations/beads-mcp/src/beads_mcp/__init__.py" \
     "$(grep '__version__ = ' integrations/beads-mcp/src/beads_mcp/__init__.py 2>/dev/null | sed 's/.*"\(.*\)".*/\1/')" \
     "MCP __init__.py"
 
-check_version ".claude-plugin/plugin.json" \
-    "$(jq -r '.version' .claude-plugin/plugin.json 2>/dev/null)" \
+check_version "claude-plugin/.claude-plugin/plugin.json" \
+    "$(jq -r '.version' claude-plugin/.claude-plugin/plugin.json 2>/dev/null)" \
     "Claude plugin.json"
 
 check_version ".claude-plugin/marketplace.json" \