docs: fix broken links, phantom script references, and stale CI description

Repairs every broken relative link in active docs (targets renamed or
archived long ago: PLUGIN_DEVELOPMENT.md -> PLUGIN_DEVELOPMENT_GUIDE.md,
API_REFERENCE.md -> REST_API_REFERENCE.md, PLUGIN_STORE_USER_GUIDE.md ->
PLUGIN_STORE_GUIDE.md, plugin_docs/ dir, TROUBLESHOOTING_QUICK_START.md,
and MIGRATION_GUIDE's README link that silently resolved to the docs
index instead of the project README). Replaces commands invoking scripts
that do not exist (scripts/update_stats.py, validate_registry.py,
check_updates.py, fix_permissions.sh) with the real tooling, and
rewrites HOW_TO_RUN_TESTS.md's CI section, which described a
security-audit workflow that was never committed and a pytest workflow
'queued to land' that landed long ago as test.yml.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SXb4mKcAkVaxkeTb3YnAdr

docs/DEVELOPER_QUICK_REFERENCE.md

@@ -31,7 +31,7 @@ POST /api/v3/system/action
 
 **Base URL**: `http://your-pi-ip:5000/api/v3`
 
-See [API_REFERENCE.md](API_REFERENCE.md) for complete documentation.
+See [REST_API_REFERENCE.md](REST_API_REFERENCE.md) for complete documentation.
 
 ## Display Manager Quick Methods
 
@@ -195,7 +195,7 @@ LEDMatrix/
 │   ├── config.json      # Main configuration
 │   └── config_secrets.json  # API keys and secrets
 ├── docs/                 # Documentation
-│   ├── API_REFERENCE.md
+│   ├── REST_API_REFERENCE.md
 │   ├── PLUGIN_API_REFERENCE.md
 │   └── ...
 └── src/
@@ -207,7 +207,7 @@ LEDMatrix/
 
 ## Quick Links
 
-- [Complete API Reference](API_REFERENCE.md)
+- [Complete REST API Reference](REST_API_REFERENCE.md)
 - [Plugin API Reference](PLUGIN_API_REFERENCE.md)
 - [Plugin Development Guide](PLUGIN_DEVELOPMENT_GUIDE.md)
 - [Advanced Patterns](ADVANCED_PLUGIN_DEVELOPMENT.md)