Update LEAME.md and align service log paths

[magdasmat]

Summary

Restructure docs/LEAME.md into a clearer, reproducible installation guide and aligns
the log paths across compose, .env and the deploy script.

Documentation (docs/LEAME.md)

• Split into Part I – Installation (numbered step-by-step flow) and
  Part II – Operations & maintenance (situational tasks), so the numbering
  reflects the real install order.
• Added a Mermaid diagram of the container architecture (Apache routing,
  service-to-DB connections, bind mounts and logs).
• Added the "why": data kept outside the repo, and the rootless permission
  model (UID mapping, ACLs, SELinux).
• New MongoDB log rotation section (logrotate + systemd --user timer,
  lingering requirement, SIGUSR1 → logRotate: reopen).
• Fixed a malformed mongosh example and added a short "what admins must
  prepare" note under Requirements.

Behavior change – log paths

MongoDB and Apache logs now live in per-service subdirectories, consistent with
PostgreSQL:

• MongoDB: ${APP_LOG_DIR}/mongo/mongod.log
• Apache: ${APP_LOG_DIR}/apache/ (removed the separate APACHE_LOG_DIR var;
  Apache now uses APP_LOG_DIR)

Updated accordingly in:

• docker-compose.yml
• .env.example
• deploy/fix_permissions.sh

Removed scripts

• Remove obsolete installation scripts load_dataset_ritools.sh and register_dataset_metadata.sh (no longer used).