[CHORE] Remove deprecated validate command — already replaced by registry-validate

[Wolfvin]

Problem

validate prints on every invocation:

DEPRECATED: `codelens validate` is renamed to `codelens registry-validate`.
The old name still works for one release cycle but will be removed.

The deprecation notice is already in place. Time to complete the removal.

Expected Fix

• Remove validate as a registered command from codelens.py
• Ensure registry-validate is documented as the canonical replacement
• Update command count (64 → 63) across README, SKILL.md, SKILL-QUICK.md, pyproject.toml, skill.json, mcp_server.py, graph_model.py — use scripts/sync_command_count.py (added in PR fix(#38): single-source-of-truth for command + MCP tool counts #90)