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>

claude-plugin/skills/beads/CLAUDE.md

@@ -66,7 +66,7 @@ After skill updates:
 
 ```bash
 # Verify SKILL.md is within token budget
-wc -w skills/beads/SKILL.md  # Target: 400-600 words
+wc -w claude-plugin/skills/beads/SKILL.md  # Target: 400-600 words
 
 # Verify links resolve
 # (Manual check: ensure all resource links in SKILL.md exist)

claude-plugin/skills/beads/README.md

@@ -107,7 +107,7 @@ NEXT: Implement rate limiting"
 
 ## Contributing
 
-This skill is maintained at [github.com/steveyegge/beads](https://github.com/steveyegge/beads) in the `skills/beads/` directory.
+This skill is maintained at [github.com/steveyegge/beads](https://github.com/steveyegge/beads) in the `claude-plugin/skills/beads/` directory.
 
 Issues and PRs welcome for:
 - Documentation improvements