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>

RELEASING.md

@@ -134,7 +134,7 @@ This updates:
 - `cmd/bd/version.go` - CLI version constant
 - `integrations/beads-mcp/pyproject.toml` - MCP server version
 - `integrations/beads-mcp/src/beads_mcp/__init__.py` - MCP Python version
-- `.claude-plugin/plugin.json` - Plugin version
+- `claude-plugin/.claude-plugin/plugin.json` - Plugin version
 - `.claude-plugin/marketplace.json` - Marketplace version
 - `npm-package/package.json` - npm package version
 - `cmd/bd/templates/hooks/*` - Git hook versions
@@ -338,11 +338,11 @@ Update the Claude Code marketplace metadata files:
 # Change version to match current release
 vim .claude-plugin/marketplace.json
 
-# Update .claude-plugin/plugin.json if needed
-vim .claude-plugin/plugin.json
+# Update claude-plugin/.claude-plugin/plugin.json if needed
+vim claude-plugin/.claude-plugin/plugin.json
 
 # Commit changes
-git add .claude-plugin/
+git add .claude-plugin/ claude-plugin/.claude-plugin/
 git commit -m "chore: Update Claude Code marketplace to v0.22.0"
 ```